<style>
  .down, .up {
    --column-height: 500px;
    --image-height: 200px;
    --row-gap: 10px;
    --num-images: 5;

    height: var(--column-height);
    overflow: hidden;
    position: relative;
    -webkit-mask-image: linear-gradient(to bottom, rgba(0, 0, 0, 0) 0%, black 20%, black 80%, rgba(0, 0, 0, 0) 100%);
  }

  .scroll-container {
    display: flex;
    flex-direction: column;
  }

  .up .scroll-container {
    animation: imagescrolling 15s linear infinite alternate;
    animation-delay: -0.1s; /* Offset to ensure it starts halfway through the cycle */
  }

  .down .scroll-container {
    animation: imagescrolling2 15s linear infinite alternate;
  }

  .scroll-container img {
    height: var(--image-height);
    width: 100%;
    margin-bottom: var(--row-gap);
    padding: 0;
    object-fit: cover;
  }

  @keyframes imagescrolling {
    0% {
      transform: translateY(0);
    }
    100% {
      transform: translateY(calc(
        -1 * (((var(--image-height) + var(--row-gap)) * var(--num-images)) - var(--column-height))
      ));
    }
  }

  @keyframes imagescrolling2 {
    0% {
      transform: translateY(calc(
        -1 * (((var(--image-height) + var(--row-gap)) * var(--num-images)) - var(--column-height))
      ));
    }
    100% {
      transform: translateY(0);
    }
  }
</style>

laravel:
composer create-project laravel/laravel nombre-proyecto
yii2:
composer create-project --prefer-dist yiisoft/yii2-app-basic basic
composer create-project --prefer-dist yiisoft/yii2-app-advanced yii-application

yii3
composer create-project yiisoft/app nombre-del-proyecto

stos comandos instalan las versiones estables más recientes y las crean listas para usar. Si se desea la última versión de desarrollo, se puede añadir la opción --stability=dev, aunque no es recomendado para producción.

La opción --stability=dev se coloca directamente en el comando de Composer al momento de crear el proyecto con create-project. Sirve para indicar que deseas instalar la versión de desarrollo (inestable) de un paquete en lugar de la versión estable por defecto.
Cómo y dónde colocar --stability=dev

Ejemplo para Yii2 Basic con la versión de desarrollo:

composer create-project --prefer-dist --stability=dev yiisoft/yii2-app-basic basic
Ejemplo para Yii2 Advanced con la versión de desarrollo:

composer create-project --prefer-dist --stability=dev yiisoft/yii2-app-advanced yii-application
Ejemplo para Yii3 con la versión de desarrollo:

composer create-project --stability=dev yiisoft/app nombre-del-proyecto
Detalles importantes
--stability=dev va después de create-project y antes del nombre del paquete o justo junto con la opción --prefer-dist.

Esta opción indica a Composer que acepte versiones con estabilidad "dev" (desarrollo), que pueden incluir cambios recientes no testeados para producción.

Si utilizas esta opción, es posible que debas también agregar --prefer-source para que Composer use el código fuente en lugar de los paquetes comprimidos.

var $sticky = $(".sticky-column").stickit({				
  scope: StickScope.Parent,				
  top: 20,
  screenMinWidth: 980
});	

$sticky.bind('stickit:end', function () {
  $('.sticky-column').addClass('bottom-0');
});
$sticky.bind('stickit:stick', function () {
  $('.sticky-column').removeClass('bottom-0');
});

https://github.com/emn178/jquery-stickit

public static function Lista()
    {
        $s = \yii\helpers\ArrayHelper::map(Transportes::find()->orderBy('id_transporte')->all(), 'id_transporte', 'desc_transporte');
        return ($s) ? $s : [];
    }

public void reverseString(char[] s) {
  char[] fixedS = s.clone();

  for (int i = 0; i < s.length; i++) {
    s[i] = fixedS[(fixedS.length - 1) - i];
  }
}

public int singleNumber(int[] nums) {
  Arrays.sort(nums);

  for (int i = 0; i < (nums.length - 1); i++) {

    if ((i == 0 && nums[i + 1] != nums[i])
        || (nums[i + 1] != nums[i] && nums[i] != nums[i - 1])){
      return nums[i];
    }
  }
  return nums[nums.length - 1];
}

tablas a:
-- Table: public.tipobuques

-- DROP TABLE IF EXISTS public.tipobuques;

CREATE TABLE IF NOT EXISTS public.tipobuques
(
    id_tipo integer NOT NULL DEFAULT nextval('tipo_buques_id_tipo_seq'::regclass),
    desc_tipo character varying COLLATE pg_catalog."default",
    otros_datos character varying(255) COLLATE pg_catalog."default",
    CONSTRAINT tipo_buques_pkey PRIMARY KEY (id_tipo)
)

TABLESPACE pg_default;

ALTER TABLE IF EXISTS public.tipobuques
    OWNER to postgres;

tabla b:
-- Table: public.transportes

-- DROP TABLE IF EXISTS public.transportes;

CREATE TABLE IF NOT EXISTS public.transportes
(
    id_transporte integer NOT NULL DEFAULT nextval('transportes_id_transporte_seq'::regclass),
    nombre_transporte character varying(255) COLLATE pg_catalog."default" NOT NULL,
    id_buquescarga integer,
    id_tipo integer[],
    id_nacionalidad integer,
    otros_datos character varying(255) COLLATE pg_catalog."default",
    CONSTRAINT transportes_pkey PRIMARY KEY (id_transporte)
)

TABLESPACE pg_default;

ALTER TABLE IF EXISTS public.transportes
    OWNER to postgres;

<div class="col-xs-4" id='id_transporte' style="display:none;">
                <?= $form->field($model, 'id_transporte')
                    ->dropDownList(
                        ArrayHelper::map(
                            Transportes::find()->all(),
                            'id_transporte',
                            'nombre_transporte'
                        ),
                        [
                            'prompt' => 'Seleccione Transporte',
                            'id' => 'id-transporte'
                        ]
                    ); ?>
            </div>

            <div class="col-xs-4" id='id_tipo' style="display:none;">
                <?= $form->field($model, 'id_tipo')->widget(\kartik\depdrop\DepDrop::classname(), [
                    'options' => ['id' => 'id-tipo'],
                    'pluginOptions' => [
                        'depends' => ['id-transporte'],
                        'placeholder' => 'Seleccione Tipo de Buque',
                        'url' => \yii\helpers\Url::to(['transportes/listartipos'])
                    ],
                ]); ?>
            </div>
functionController:
public function actionListartipos()
{
    \Yii::$app->response->format = \yii\web\Response::FORMAT_JSON;
    
    $out = [];
    
    if (isset($_POST['depdrop_parents'])) {
        $id_transporte = $_POST['depdrop_parents'][0];
        
        if (!empty($id_transporte)) {
            // Buscar el transporte seleccionado
            $transporte = \app\models\Transportes::findOne($id_transporte);
            
            if ($transporte && !empty($transporte->id_tipo)) {
                // Convertir el array PostgreSQL a un array de PHP
                $ids_tipos = $transporte->id_tipo;
                
                // Si es una cadena (formato PostgreSQL array), convertir a array
                if (is_string($ids_tipos)) {
                    // Remover llaves y convertir a array
                    $ids_tipos = trim($ids_tipos, '{}');
                    $ids_tipos = $ids_tipos ? explode(',', $ids_tipos) : [];
                }
                
                if (!empty($ids_tipos)) {
                    // Buscar los tipos de buques correspondientes a los IDs en el array
                    $out = \app\models\Tipobuques::find()
                        ->where(['id_tipo' => $ids_tipos])
                        ->select(['id_tipo as id', 'desc_tipo as name'])
                        ->asArray()
                        ->all();
                }
            }
        }
    }
    
    return ['output' => $out, 'selected' => ''];
}

use kartik\select2\Select2;

<?= $form->field($model, 'id_tipo')->widget(Select2::classname(), [
    'data' => ArrayHelper::map(Tipobuques::find()->all(), 'id_tipo', 'desc_tipo'),
    'options' => [
        'multiple' => true,
        'placeholder' => 'Seleccione Tipos de Buque...'
    ],
]); ?>
  
index:
[
  'attribute' => 'id_tipo',
  'label' => 'Tipos de Buques',
  'value' => function ($model) {
    // Usar el método de debug seguro
    return $model->getTiposBuquesNombres();
  },
  'format' => 'raw',
],
view:
[
  'attribute' => 'id_tipo',
  'label' => 'Tipos de Buques',
  'value' => function ($model) {
    // Usar el método de debug seguro
    return $model->getTiposBuquesNombres();
  },
    'format' => 'raw',
      ],

public boolean containsDuplicate(int[] nums) {

  Set<Integer> set = new HashSet<>();

  for (int num : nums) {
    if (!set.add(num)) {
      return true;
    }
  }
  return false;
}

public void rotate(int[]nums, int k) {
  int n = nums.length;
  int[] newNums = new int[n];
  k = k % n;// k is number of rotations
  
  for(int i = 0; i < n; i++) {
    newNums[(i + k) % n] = nums[i];
  }
  
  for(int i = 0; i < n; i++){
    nums[1] = newNums[i];
  }
}

.wcgs-grid-template.wcgs-grid-height-auto.grid.wcgs-grid-template > *:only-child {
  grid-column: 1 / -1;
}
 

document.addEventListener("DOMContentLoaded", function() {
        var mediaQuery = window.matchMedia("(min-width: 641px)");
 
        function handleChange(e) {
            if (e.matches) {
                var el = document.querySelector(".fusion-no-medium-visibility.fusion-no-large-visibility #wpgs-gallery");
                if (el) {
                    el.remove();
                }
            }
        }
 
        // Run once
        handleChange(mediaQuery);
 
        // Run when screen crosses 641px breakpoint
        mediaQuery.addEventListener("change", handleChange);
});

DO $$
BEGIN
   IF NOT EXISTS (
      SELECT 1 
      FROM pg_class c
      JOIN pg_namespace n ON n.oid = c.relnamespace
      WHERE c.relname = 'carrier_id_seq'
        AND n.nspname = 'lookup'
   ) THEN
      CREATE SEQUENCE lookup.carrier_id_seq OWNED BY lookup.carrier.id;
   END IF;
END$$;

-- Make id use sequence
ALTER TABLE lookup.carrier ALTER COLUMN id SET DEFAULT nextval('lookup.carrier_id_seq');

-- Reset sequence based on max(id) from lookup.carrier
SELECT setval(
   'lookup.carrier_id_seq',
   (SELECT COALESCE(MAX(id), 0) + 1 FROM lookup.carrier),
   false
);




-- Create a sequence if not exists
DO $$
BEGIN
   IF NOT EXISTS (SELECT 1 FROM pg_class WHERE relname = 'carrier_id_seq') THEN
      CREATE SEQUENCE carrier_id_seq OWNED BY carrier.id;
   END IF;
END$$;

-- Make id use sequence
ALTER TABLE carrier ALTER COLUMN id SET DEFAULT nextval('carrier_id_seq');


SELECT setval('carrier_id_seq', (SELECT COALESCE(MAX(id), 0) + 1 FROM carrier), false);

# Commands to add  Jar file to postgres
nano ~/.bashrc

# Add PostgreSQL JDBC JAR to Spark
export SPARK_CLASSPATH=$SPARK_CLASSPATH:/home/youruser/jars/postgresql-42.7.3.jar
export PYSPARK_SUBMIT_ARGS="--jars /home/youruser/jars/postgresql-42.7.3.jar pyspark-shell"

source ~/.bashrc

# Restart your terminal or Jupyter Notebook server to apply the changes.

// import 'package:flutter/material.dart';

// class GamingPage extends StatelessWidget {
//   const GamingPage({super.key});

//   @override
//   Widget build(BuildContext context) {
//     final games = [
//       {"title": "چرخونه شانس", "icon": Icons.casino},
//       {"title": "جعبه جایزه", "icon": Icons.card_giftcard},
//       {"title": "چیستان", "icon": Icons.quiz},
//       {"title": "حدس کلمه", "icon": Icons.spellcheck},
//       {"title": "بازی حافظه", "icon": Icons.memory},
//       {"title": "پازل", "icon": Icons.extension},
//     ];

//     return Directionality(
//       textDirection: TextDirection.rtl,
//       child: Scaffold(
//         body: CustomScrollView(
//           slivers: [
//             // 🔹 هدر بزرگ که کوچیک میشه
//             SliverAppBar(
//               expandedHeight: 200,
//               pinned: true,
//               floating: false,
//               flexibleSpace: FlexibleSpaceBar(
//                 title: const Text("🎮 بازی‌ها"),
//                 background: Container(
//                   decoration: const BoxDecoration(
//                     gradient: LinearGradient(
//                       colors: [Color(0xFF6A11CB), Color(0xFF2575FC)],
//                       begin: Alignment.topRight,
//                       end: Alignment.bottomLeft,
//                     ),
//                   ),
//                   child: Center(
//                     child: Icon(
//                       Icons.videogame_asset,
//                       size: 80,
//                       color: Colors.white.withOpacity(0.8),
//                     ),
//                   ),
//                 ),
//               ),
//             ),

//             // 🔹 Grid بازی‌ها
//             SliverPadding(
//               padding: const EdgeInsets.all(16),
//               sliver: SliverGrid(
//                 gridDelegate: const SliverGridDelegateWithFixedCrossAxisCount(
//                   crossAxisCount: 2, // دو ستون
//                   mainAxisSpacing: 16,
//                   crossAxisSpacing: 16,
//                   childAspectRatio: 1, // مربعی
//                 ),
//                 delegate: SliverChildBuilderDelegate(
//                   (context, index) {
//                     final game = games[index];
//                     return _gameCard(
//                       context,
//                       game["title"] as String,
//                       game["icon"] as IconData,
//                     );
//                   },
//                   childCount: games.length,
//                 ),
//               ),
//             ),
//           ],
//         ),
//       ),
//     );
//   }

//   Widget _gameCard(BuildContext context, String title, IconData icon) {
//     return InkWell(
//       onTap: () {
//         ScaffoldMessenger.of(context).showSnackBar(
//           SnackBar(content: Text("شروع بازی: $title")),
//         );
//       },
//       child: Card(
//         shape: RoundedRectangleBorder(borderRadius: BorderRadius.circular(16)),
//         elevation: 4,
//         child: Column(
//           mainAxisAlignment: MainAxisAlignment.center,
//           children: [
//             Icon(icon, size: 50, color: Colors.deepPurple),
//             const SizedBox(height: 12),
//             Text(
//               title,
//               style: const TextStyle(fontSize: 16, fontWeight: FontWeight.w600),
//             ),
//           ],
//         ),
//       ),
//     );
//   }
// }

/**
 * !عالی
 * 
 * 
 */
// import 'package:flutter/material.dart';

// class GamingPage extends StatelessWidget {
//   const GamingPage({super.key});

//   @override
//   Widget build(BuildContext context) {
//     final games = [
//       {"title": "چرخونه شانس", "icon": Icons.casino},
//       {"title": "جعبه جایزه", "icon": Icons.card_giftcard},
//       {"title": "چیستان", "icon": Icons.quiz},
//       {"title": "حدس کلمه", "icon": Icons.spellcheck},
//       {"title": "بازی حافظه", "icon": Icons.memory},
//       {"title": "پازل", "icon": Icons.extension},
//     ];

//     return Directionality(
//       textDirection: TextDirection.rtl,
//       child: Scaffold(
//         body: CustomScrollView(
//           slivers: [
//             // 🔹 هدر تصویری
//             SliverAppBar(
//               expandedHeight: 220,
//               pinned: true,
//               flexibleSpace: FlexibleSpaceBar(
//                 title: const Text("🎮 بازی‌ها"),
//                 centerTitle: true,
//                 background: Image.asset(
//                   "assets/gaming_banner.jpg", // عکس بنر بزرگ
//                   fit: BoxFit.cover,
//                 ),
//               ),
//             ),

//             // 🔹 Grid بازی‌ها
//             SliverPadding(
//               padding: const EdgeInsets.all(16),
//               sliver: SliverGrid(
//                 gridDelegate: const SliverGridDelegateWithFixedCrossAxisCount(
//                   crossAxisCount: 2, // دو ستون
//                   mainAxisSpacing: 16,
//                   crossAxisSpacing: 16,
//                   childAspectRatio: 1, // مربعی دقیق
//                 ),
//                 delegate: SliverChildBuilderDelegate(
//                   (context, index) {
//                     final game = games[index];
//                     return _gameCard(
//                       context,
//                       game["title"] as String,
//                       game["icon"] as IconData,
//                     );
//                   },
//                   childCount: games.length,
//                 ),
//               ),
//             ),
//           ],
//         ),
//       ),
//     );
//   }

//   Widget _gameCard(BuildContext context, String title, IconData icon) {
//     return InkWell(
//       onTap: () {
//         ScaffoldMessenger.of(context).showSnackBar(
//           SnackBar(content: Text("شروع بازی: $title")),
//         );
//       },
//       child: Card(
//         shape: RoundedRectangleBorder(borderRadius: BorderRadius.circular(16)),
//         elevation: 4,
//         child: Column(
//           mainAxisAlignment: MainAxisAlignment.center,
//           children: [
//             Icon(icon, size: 50, color: Colors.deepPurple),
//             const SizedBox(height: 12),
//             Text(
//               title,
//               style: const TextStyle(fontSize: 16, fontWeight: FontWeight.w600),
//             ),
//           ],
//         ),
//       ),
//     );
//   }
// }
import 'package:flutter/material.dart';
import 'package:lottery_app/games/memory_page.dart';

class GamingPage extends StatelessWidget {
  const GamingPage({super.key});

  @override
  Widget build(BuildContext context) {
    final games = [
      {"title": "بازی حافظه", "icon": Icons.memory},
      {"title": "تاس شانس", "icon": Icons.casino},
      {"title": "جعبه جایزه", "icon": Icons.card_giftcard},
      {"title": "چیستان", "icon": Icons.quiz},
      // {"title": "حدس کلمه", "icon": Icons.spellcheck},
      // {"title": "بازی حافظه", "icon": Icons.memory},
      // {"title": "پازل", "icon": Icons.extension},
      // {"title": "پازل", "icon": Icons.extension},
      // {"title": "پازل", "icon": Icons.extension},
    ];

    return Directionality(
      textDirection: TextDirection.rtl,
      child: Scaffold(
        body: CustomScrollView(
          slivers: [
            // 🔹 SliverAppBar با Parallax و Rounded Bottom
            SliverAppBar(
              expandedHeight: 260,
              pinned: true,
              stretch: true,
              //snap: false,
              backgroundColor: const Color.fromARGB(235, 0, 0, 0),
              flexibleSpace: FlexibleSpaceBar(
                title: const Text(
                  "🎮 بازی‌ها",
                  style: TextStyle(
                    color: Colors.white,
                    fontWeight: FontWeight.bold,
                  ),
                ),
                centerTitle: true,
                stretchModes: const [
                  StretchMode.zoomBackground,
                  StretchMode.fadeTitle,
                ],
                background: Stack(
                  fit: StackFit.expand,
                  children: [
                    // تصویر پس‌زمینه
                    ClipRRect(
                      borderRadius: const BorderRadius.only(
                        bottomLeft: Radius.circular(30),
                        bottomRight: Radius.circular(30),
                      ),
                      child: Image.asset(
                        "assets/gaming_banner.jpg",
                        fit: BoxFit.cover,
                      ),
                    ),
                    // Overlay Gradient
                    Container(
                      decoration: BoxDecoration(
                        borderRadius: const BorderRadius.only(
                          bottomLeft: Radius.circular(30),
                          bottomRight: Radius.circular(30),
                        ),
                        gradient: LinearGradient(
                          colors: [
                            Colors.black.withOpacity(0.4),
                            Colors.transparent,
                          ],
                          begin: Alignment.bottomCenter,
                          end: Alignment.topCenter,
                        ),
                      ),
                    ),
                  ],
                ),
              ),
            ),

            // 🔹 Grid بازی‌ها
            SliverPadding(
              padding: const EdgeInsets.all(16),
              sliver: SliverGrid(
                gridDelegate: const SliverGridDelegateWithFixedCrossAxisCount(
                  crossAxisCount: 2,
                  mainAxisSpacing: 16,
                  crossAxisSpacing: 16,
                  childAspectRatio: 1, // مربع دقیق
                ),
                delegate: SliverChildBuilderDelegate((context, index) {
                  final game = games[index];
                  return _gameCard(
                    context,
                    game["title"] as String,
                    game["icon"] as IconData,
                  );
                }, childCount: games.length),
              ),
            ),
          ],
        ),
      ),
    );
  }

  Widget _gameCard(BuildContext context, String title, IconData icon) {
    return InkWell(
      onTap: () {
        ScaffoldMessenger.of(
          context,
        ).showSnackBar(SnackBar(content: Text("شروع بازی: $title")));
      },
      child: Card(
        shape: RoundedRectangleBorder(borderRadius: BorderRadius.circular(16)),
        elevation: 4,
        child: Column(
          mainAxisAlignment: MainAxisAlignment.center,
          children: [
            Icon(icon, size: 50, color: Colors.deepPurple),
            const SizedBox(height: 12),
            Text(
              title,
              style: const TextStyle(fontSize: 16, fontWeight: FontWeight.w600),
            ),
          ],
        ),
      ),
    );
  }
}

// import 'package:flutter/material.dart';

// class GamingPage extends StatelessWidget {
//   const GamingPage({super.key});

//   @override
//   Widget build(BuildContext context) {
//     final games = [
//       {"title": "چرخونه شانس", "icon": Icons.casino},
//       {"title": "جعبه جایزه", "icon": Icons.card_giftcard},
//       {"title": "چیستان", "icon": Icons.quiz},
//       {"title": "حدس کلمه", "icon": Icons.spellcheck},
//       {"title": "بازی حافظه", "icon": Icons.memory},
//       {"title": "پازل", "icon": Icons.extension},
//     ];

//     return Directionality(
//       textDirection: TextDirection.rtl,
//       child: Scaffold(
//         body: CustomScrollView(
//           slivers: [
//             // 🔹 هدر بزرگ که کوچیک میشه
//             SliverAppBar(
//               expandedHeight: 200,
//               pinned: true,
//               floating: false,
//               flexibleSpace: FlexibleSpaceBar(
//                 title: const Text("🎮 بازی‌ها"),
//                 background: Container(
//                   decoration: const BoxDecoration(
//                     gradient: LinearGradient(
//                       colors: [Color(0xFF6A11CB), Color(0xFF2575FC)],
//                       begin: Alignment.topRight,
//                       end: Alignment.bottomLeft,
//                     ),
//                   ),
//                   child: Center(
//                     child: Icon(
//                       Icons.videogame_asset,
//                       size: 80,
//                       color: Colors.white.withOpacity(0.8),
//                     ),
//                   ),
//                 ),
//               ),
//             ),

//             // 🔹 Grid بازی‌ها
//             SliverPadding(
//               padding: const EdgeInsets.all(16),
//               sliver: SliverGrid(
//                 gridDelegate: const SliverGridDelegateWithFixedCrossAxisCount(
//                   crossAxisCount: 2, // دو ستون
//                   mainAxisSpacing: 16,
//                   crossAxisSpacing: 16,
//                   childAspectRatio: 1, // مربعی
//                 ),
//                 delegate: SliverChildBuilderDelegate(
//                   (context, index) {
//                     final game = games[index];
//                     return _gameCard(
//                       context,
//                       game["title"] as String,
//                       game["icon"] as IconData,
//                     );
//                   },
//                   childCount: games.length,
//                 ),
//               ),
//             ),
//           ],
//         ),
//       ),
//     );
//   }

//   Widget _gameCard(BuildContext context, String title, IconData icon) {
//     return InkWell(
//       onTap: () {
//         ScaffoldMessenger.of(context).showSnackBar(
//           SnackBar(content: Text("شروع بازی: $title")),
//         );
//       },
//       child: Card(
//         shape: RoundedRectangleBorder(borderRadius: BorderRadius.circular(16)),
//         elevation: 4,
//         child: Column(
//           mainAxisAlignment: MainAxisAlignment.center,
//           children: [
//             Icon(icon, size: 50, color: Colors.deepPurple),
//             const SizedBox(height: 12),
//             Text(
//               title,
//               style: const TextStyle(fontSize: 16, fontWeight: FontWeight.w600),
//             ),
//           ],
//         ),
//       ),
//     );
//   }
// }

/**
 * !عالی
 * 
 * 
 */
// import 'package:flutter/material.dart';

// class GamingPage extends StatelessWidget {
//   const GamingPage({super.key});

//   @override
//   Widget build(BuildContext context) {
//     final games = [
//       {"title": "چرخونه شانس", "icon": Icons.casino},
//       {"title": "جعبه جایزه", "icon": Icons.card_giftcard},
//       {"title": "چیستان", "icon": Icons.quiz},
//       {"title": "حدس کلمه", "icon": Icons.spellcheck},
//       {"title": "بازی حافظه", "icon": Icons.memory},
//       {"title": "پازل", "icon": Icons.extension},
//     ];

//     return Directionality(
//       textDirection: TextDirection.rtl,
//       child: Scaffold(
//         body: CustomScrollView(
//           slivers: [
//             // 🔹 هدر تصویری
//             SliverAppBar(
//               expandedHeight: 220,
//               pinned: true,
//               flexibleSpace: FlexibleSpaceBar(
//                 title: const Text("🎮 بازی‌ها"),
//                 centerTitle: true,
//                 background: Image.asset(
//                   "assets/gaming_banner.jpg", // عکس بنر بزرگ
//                   fit: BoxFit.cover,
//                 ),
//               ),
//             ),

//             // 🔹 Grid بازی‌ها
//             SliverPadding(
//               padding: const EdgeInsets.all(16),
//               sliver: SliverGrid(
//                 gridDelegate: const SliverGridDelegateWithFixedCrossAxisCount(
//                   crossAxisCount: 2, // دو ستون
//                   mainAxisSpacing: 16,
//                   crossAxisSpacing: 16,
//                   childAspectRatio: 1, // مربعی دقیق
//                 ),
//                 delegate: SliverChildBuilderDelegate(
//                   (context, index) {
//                     final game = games[index];
//                     return _gameCard(
//                       context,
//                       game["title"] as String,
//                       game["icon"] as IconData,
//                     );
//                   },
//                   childCount: games.length,
//                 ),
//               ),
//             ),
//           ],
//         ),
//       ),
//     );
//   }

//   Widget _gameCard(BuildContext context, String title, IconData icon) {
//     return InkWell(
//       onTap: () {
//         ScaffoldMessenger.of(context).showSnackBar(
//           SnackBar(content: Text("شروع بازی: $title")),
//         );
//       },
//       child: Card(
//         shape: RoundedRectangleBorder(borderRadius: BorderRadius.circular(16)),
//         elevation: 4,
//         child: Column(
//           mainAxisAlignment: MainAxisAlignment.center,
//           children: [
//             Icon(icon, size: 50, color: Colors.deepPurple),
//             const SizedBox(height: 12),
//             Text(
//               title,
//               style: const TextStyle(fontSize: 16, fontWeight: FontWeight.w600),
//             ),
//           ],
//         ),
//       ),
//     );
//   }
// }
import 'package:flutter/material.dart';
import 'package:lottery_app/games/memory_page.dart';
import 'package:lottery_app/games/slotmachine_data.dart';
import 'package:lottery_app/games/time_game_page.dart';
import 'package:lottery_app/games/tuch_game_page.dart';

class GamingPage extends StatelessWidget {
  const GamingPage({super.key});

  @override
  Widget build(BuildContext context) {
    final games = [
      {"title": "بازی حافظه", "icon": Icons.memory},
      {"title": "ماشین شانس", "icon": Icons.casino},
      {"title": "بازی تایم", "icon": Icons.timer_off_outlined},
      {"title": "بازی تعداد کلیک", "icon": Icons.touch_app},
      // {"title": "حدس کلمه", "icon": Icons.spellcheck},
      // {"title": "بازی حافظه", "icon": Icons.memory},
      // {"title": "پازل", "icon": Icons.extension},
      // {"title": "پازل", "icon": Icons.extension},
      // {"title": "پازل", "icon": Icons.extension},
    ];

    return Directionality(
      textDirection: TextDirection.rtl,
      child: Scaffold(
        body: CustomScrollView(
          slivers: [
            // 🔹 SliverAppBar با Parallax و Rounded Bottom
            SliverAppBar(
              expandedHeight: 260,
              pinned: true,
              stretch: true,
              //snap: false,
              backgroundColor: const Color.fromARGB(235, 0, 0, 0),
              flexibleSpace: FlexibleSpaceBar(
                title: const Text(
                  "🎮 بازی‌ها",
                  style: TextStyle(
                    color: Colors.white,
                    fontWeight: FontWeight.bold,
                  ),
                ),
                centerTitle: true,
                stretchModes: const [
                  StretchMode.zoomBackground,
                  StretchMode.fadeTitle,
                ],
                background: Stack(
                  fit: StackFit.expand,
                  children: [
                    // تصویر پس‌زمینه
                    ClipRRect(
                      borderRadius: const BorderRadius.only(
                        bottomLeft: Radius.circular(30),
                        bottomRight: Radius.circular(30),
                      ),
                      child: Image.asset(
                        "assets/gaming_banner.jpg",
                        fit: BoxFit.cover,
                      ),
                    ),
                    // Overlay Gradient
                    Container(
                      decoration: BoxDecoration(
                        borderRadius: const BorderRadius.only(
                          bottomLeft: Radius.circular(30),
                          bottomRight: Radius.circular(30),
                        ),
                        gradient: LinearGradient(
                          colors: [
                            Colors.black.withOpacity(0.4),
                            Colors.transparent,
                          ],
                          begin: Alignment.bottomCenter,
                          end: Alignment.topCenter,
                        ),
                      ),
                    ),
                  ],
                ),
              ),
            ),

            // 🔹 Grid بازی‌ها
            SliverPadding(
              padding: const EdgeInsets.all(16),
              sliver: SliverGrid(
                gridDelegate: const SliverGridDelegateWithFixedCrossAxisCount(
                  crossAxisCount: 2,
                  mainAxisSpacing: 16,
                  crossAxisSpacing: 16,
                  childAspectRatio: 1, // مربع دقیق
                ),
                delegate: SliverChildBuilderDelegate((context, index) {
                  final game = games[index];
                  return _gameCard(
                    context,
                    game["title"] as String,
                    game["icon"] as IconData,
                  );
                }, childCount: games.length),
              ),
            ),
          ],
        ),
      ),
    );
  }

  Widget _gameCard(BuildContext context, String title, IconData icon) {
    return InkWell(
      onTap: () {
        Widget page;

        switch (title) {
          case "بازی حافظه":
            page = MemoryTilesApp(); // صفحه مخصوص شطرنج
            break;
          case "ماشین شانس":
            page = SlotMachineGame(); // صفحه مخصوص فوتبال
            break;
          case "بازی تایم":
            page = TimeGamePage(); // صفحه مخصوص پازل
            break;
          case "بازی تعداد کلیک":
            page = TouchGameApp(); // صفحه مخصوص پازل
            break;
          default:
            page = GamingPage(); // fallback در صورتی که اسم بازی ناشناخته باشه
        }

// رفتن به صفحه بعدی
Navigator.push(
  context,
  MaterialPageRoute(builder: (context) => page),
);
      },
      child: Card(
        shape: RoundedRectangleBorder(borderRadius: BorderRadius.circular(16)),
        elevation: 4,
        child: Column(
          mainAxisAlignment: MainAxisAlignment.center,
          children: [
            Icon(icon, size: 50, color: Colors.deepPurple),
            const SizedBox(height: 12),
            Text(
              title,
              style: const TextStyle(fontSize: 16, fontWeight: FontWeight.w600),
            ),
          ],
        ),
      ),
    );
  }
}

#!/bin/bash
# Jobran Rodriguez

# Definir lista de personas (en orden) con 8 nombres
persons=("Juan" "Jobran" "Luis" "Jose" "Gabriel" "Jonathan" "Brian" "Robert")

# Detectar carpeta de escritorio válida
if [ -d "$HOME/Escritorio" ]; then
    DESKTOP_DIR="$HOME/Escritorio"
elif [ -d "$HOME/Desktop" ]; then
    DESKTOP_DIR="$HOME/Desktop"
else
    DESKTOP_DIR="$HOME/Escritorio"
    mkdir -p "$DESKTOP_DIR"
    echo "No se encontró carpeta de escritorio, se ha creado '$DESKTOP_DIR'."
fi

# Crear carpeta asignacion
A="$DESKTOP_DIR/asignacion"
mkdir -p "$A"

# Definir archivo de salida
OUTPUT_FILE="$A/asignacion_caja.txt"

echo "Hola! Este script te dirá qué días te toca buscar la caja de comida este mes."
read -p "Por favor, ingresa tu nombre: " name

# Validar mes
while true; do
    read -p "Ingresa el número del mes (1-12): " month
    if [[ "$month" =~ ^[0-9]+$ ]] && (( month >= 1 && month <= 12 )); then
        # Eliminar ceros a la izquierda para cálculos
        month=$((10#$month))
        # Formatear para mostrar
        month_fmt=$(printf "%02d" $month)
        break
    else
        echo "Error: Debes ingresar un número válido entre 1 y 12 para el mes."
    fi
done

# Validar año
while true; do
    read -p "Ingresa el año (ej. 2025): " year
    if [[ "$year" =~ ^[0-9]{4}$ ]] && (( year >= 1900 && year <= 3000 )); then
        break
    else
        echo "Error: Debes ingresar un año válido de 4 dígitos (por ejemplo, 2023)."
    fi
done

# Verificar nombre con mensaje específico
index=-1
for i in "${!persons[@]}"; do
    if [[ "${persons[$i],,}" == "${name,,}" ]]; then
        index=$i
        break
    fi
done

if [ $index -eq -1 ]; then
    echo "Error: Debes ingresar un nombre válido de las personas que trabajan en la oficina de sistemas y usan el servicio del comedor."
    echo "Nombres válidos: ${persons[*]}"
    exit 1
fi

# Fecha actual (sin ceros a la izquierda para comparaciones)
current_year=$(date +%Y)
current_month=$(date +%-m)
current_day=$(date +%-d)

# Determinar si mostrar asignación individual
show_individual=1
if (( year < current_year )) || { (( year == current_year )) && (( month < current_month )); }; then
    show_individual=0
fi

# Función para obtener días del mes
days_in_month() {
    local m=$1
    local y=$2
    
    case $m in
        1|3|5|7|8|10|12) echo 31 ;;
        4|6|9|11) echo 30 ;;
        2)
            if (( (y % 400 == 0) || ((y % 4 == 0) && (y % 100 != 0)) )); then
                echo 29
            else
                echo 28
            fi
            ;;
        *)
            echo 30
            ;;
    esac
}

total_days=$(days_in_month $month $year)

# Pre-calcular días laborales y asignaciones
declare -a laboral_days
declare -a asignacion_personas
declare -a day_names
laboral_count=0

for (( day=1; day<=total_days; day++ )); do
    # Formatear día con dos dígitos para fecha
    day_fmt=$(printf "%02d" $day)
    wd=$(date -d "$year-$month_fmt-$day_fmt" +%u 2>/dev/null)
    
    if [ $? -ne 0 ]; then
        echo "Error: Fecha inválida $year-$month_fmt-$day_fmt. Verifica el mes y año."
        exit 1
    fi
    
    if (( wd >= 1 && wd <= 5 )); then
        laboral_days[laboral_count]=$day
        assign_index=$(( laboral_count % ${#persons[@]} ))
        asignacion_personas[laboral_count]=${persons[$assign_index]}
        
        # Obtener nombre del día en español
        day_name=$(LC_TIME=es_ES.UTF-8 date -d "$year-$month_fmt-$day_fmt" +%A 2>/dev/null)
        day_names[laboral_count]=$day_name
        
        ((laboral_count++))
    fi
done

# Crear o sobreescribir archivo
echo "Asignación de búsqueda de caja para $month_fmt/$year" > "$OUTPUT_FILE"
echo "--------------------------------------------" >> "$OUTPUT_FILE"

assigned_days=()
current_week=""
week_started=0

# Mostrar asignación semanal por pantalla
echo
echo "📅 Asignación semanal de búsqueda de caja para $month_fmt/$year:"
echo "=========================================================="

for (( i=0; i<laboral_count; i++ )); do
    day=${laboral_days[i]}
    assigned_person=${asignacion_personas[i]}
    day_name=${day_names[i]}
    
    # Formatear día con dos dígitos
    day_fmt=$(printf "%02d" $day)
    fecha_es=$(LC_TIME=es_ES.UTF-8 date -d "$year-$month_fmt-$day_fmt" +"%A %d de %B de %Y" 2>/dev/null)
    
    if [ $? -ne 0 ]; then
        echo "Error: No se pudo obtener información de fecha para $year-$month_fmt-$day_fmt"
        continue
    fi
    
    # Determinar semana actual
    week_num=$(date -d "$year-$month_fmt-$day_fmt" +%U 2>/dev/null)
    
    # Verificar si la fecha ya pasó
    date_passed=0
    if (( year < current_year )) || \
       { (( year == current_year )) && (( month < current_month )); } || \
       { (( year == current_year )) && (( month == current_month )) && (( day < current_day )); }; then
        date_passed=1
    fi
    
    # Escribir en archivo (todas las fechas)
    echo "$fecha_es : $assigned_person" >> "$OUTPUT_FILE"
    
    # Mostrar solo asignación individual para el usuario si corresponde
    if [[ "${assigned_person,,}" == "${name,,}" && show_individual -eq 1 ]]; then
        assigned_days+=("$fecha_es")
    fi
    
    # Mostrar asignación semanal por pantalla (solo fechas futuras o actual)
    if [ $date_passed -eq 0 ]; then
        if [ "$current_week" != "$week_num" ]; then
            if [ $week_started -eq 1 ]; then
                echo "----------------------------------------------------"
            fi
            current_week=$week_num
            week_start_date=$(date -d "$year-$month_fmt-$day_fmt -$(( $(date -d "$year-$month_fmt-$day_fmt" +%u) - 1 )) days" +"%d/%m" 2>/dev/null)
            week_end_date=$(date -d "$year-$month_fmt-$day_fmt +$(( 7 - $(date -d "$year-$month_fmt-$day_fmt" +%u) )) days" +"%d/%m" 2>/dev/null)
            echo "📋 Semana del $week_start_date al $week_end_date:"
            week_started=1
        fi
        
        # Icono según el día de la semana
        case $day_name in
            lunes) icon="🔵" ;;
            martes) icon="🟢" ;;
            miércoles|miercoles) icon="🟡" ;;
            jueves) icon="🟠" ;;
            viernes) icon="🔴" ;;
            *) icon="📌" ;;
        esac
        
        # Resaltar si es el usuario actual
        if [[ "${assigned_person,,}" == "${name,,}" ]]; then
            echo "   $icon $day_name $day: 👤 **TÚ**"
        else
            echo "   $icon $day_name $day: $assigned_person"
        fi
    fi
done

if [ $week_started -eq 1 ]; then
    echo "=========================================================="
fi

# Mostrar resultados individuales al usuario
if (( show_individual == 1 )); then
    echo
    echo "¡Hola, $name! 🎉 Aquí están los días que te toca buscar la caja de comida este mes:"
    if [ ${#assigned_days[@]} -eq 0 ]; then
        echo "¡Nada esta vez! Pero recuerda estar listo para la próxima ronda. 😉"
    else
        for d in "${assigned_days[@]}"; do
            echo "  - $d"
        done
    fi
else
    echo
    echo "Tu asignación individual no se mostrará porque el mes seleccionado ($month_fmt/$year) ya pasó."
fi

echo
echo "Además, se ha creado o actualizado el archivo con la asignación completa en:"
echo "  $OUTPUT_FILE"
echo
echo "¡Gracias por colaborar con el equipo! 💪🍱"

exit 0

public int maxProfit(int[] prices) {
  int maxProfit = 0;

  for (int i = 1; i < prices.lentgh; i++) {
    if (prices[i] > prices[i -1]) {
      maxProfit += (prices[i] - prices[i -1]);
    }
  }
  return maxProfit;
}

git config --global url."https://github.com/".insteadOf git@github.com

composer audit 

 "require-dev": {
        "yiisoft/yii2-debug": "~2.1.0",
        "yiisoft/yii2-gii": "~2.1.0",
        "yiisoft/yii2-faker": "~2.0.0",
        "codeception/base": "^2.4.0",
        "phpunit/phpunit": "~6.5.5",
        "codeception/verify": "~1.0.0",
        "symfony/browser-kit": ">=2.7 <=4.2.4"
    },
      "config": {
        "process-timeout": 1800,
         "discard-changes": true,
	 "platform": {
      "php": "7.4.33"
	},
       "allow-plugins": {
            "yiisoft/yii2-composer": true
        }
    },

import 'package:flutter/material.dart';
import 'package:flutter_map/flutter_map.dart';
import 'package:provider/provider.dart';

/// Data model for the user's mission and simulated location.
class MissionData extends ChangeNotifier {
  final double _totalDistanceKm;
  double _currentDistanceKm;
  final double _userLatitude;
  final double _userLongitude;

  /// Initializes the mission with a total distance and a simulated user location.
  ///
  /// The initial current distance walked is 0.0.
  MissionData({
    required double totalDistanceKm,
    required double userLatitude,
    required double userLongitude,
    double initialDistanceKm = 0.0,
  })  : _totalDistanceKm = totalDistanceKm,
        _userLatitude = userLatitude,
        _userLongitude = userLongitude,
        _currentDistanceKm = initialDistanceKm {
    if (_totalDistanceKm <= 0) {
      throw ArgumentError('Total distance must be positive.');
    }
    if (_currentDistanceKm < 0) {
      throw ArgumentError('Initial distance cannot be negative.');
    }
    if (_currentDistanceKm > _totalDistanceKm) {
      _currentDistanceKm = _totalDistanceKm; // Cap initial distance at total
    }
  }

  /// The total distance required for the mission in kilometers.
  double get totalDistanceKm => _totalDistanceKm;

  /// The current distance walked by the user in kilometers.
  double get currentDistanceKm => _currentDistanceKm;

  /// The simulated geographical latitude of the user.
  double get userLatitude => _userLatitude;

  /// The simulated geographical longitude of the user.
  double get userLongitude => _userLongitude;

  /// The remaining distance to complete the mission in kilometers.
  double get remainingDistanceKm =>
      (_totalDistanceKm - _currentDistanceKm).clamp(0.0, _totalDistanceKm);

  /// The progress of the mission as a percentage (0.0 to 1.0).
  double get progressPercentage =>
      _currentDistanceKm / _totalDistanceKm.clamp(1.0, double.infinity);

  /// Adds a specified [distance] in kilometers to the current distance walked.
  ///
  /// The distance added must be positive. The current distance will not exceed
  /// the total mission distance.
  void addDistance(double distance) {
    if (distance <= 0) {
      throw ArgumentError('Distance to add must be positive.');
    }
    _currentDistanceKm = (_currentDistanceKm + distance).clamp(0.0, _totalDistanceKm);
    notifyListeners();
  }
}

/// The main application widget for displaying location and mission.
class LocationMissionApp extends StatelessWidget {
  const LocationMissionApp({super.key});

  @override
  Widget build(BuildContext context) {
    return ChangeNotifierProvider<MissionData>(
      create: (context) => MissionData(
        totalDistanceKm: 100.0, // Mission: walk 100 kilometers
        userLatitude: 51.5, // Simulated London latitude
        userLongitude: -0.09, // Simulated London longitude
      ),
      builder: (context, child) {
        return MaterialApp(
          title: 'Mission Tracker',
          theme: ThemeData(
            primarySwatch: Colors.blue,
            visualDensity: VisualDensity.adaptivePlatformDensity,
          ),
          home: const MissionScreen(),
        );
      },
    );
  }
}

/// Displays the map with simulated user location and mission progress.
class MissionScreen extends StatefulWidget {
  const MissionScreen({super.key});

  @override
  State<MissionScreen> createState() => _MissionScreenState();
}

class _MissionScreenState extends State<MissionScreen> {
  final TextEditingController _distanceInputController = TextEditingController();
  final _formKey = GlobalKey<FormState>();

  @override
  void dispose() {
    _distanceInputController.dispose();
    super.dispose();
  }

  @override
  Widget build(BuildContext context) {
    return Scaffold(
      appBar: AppBar(
        title: const Text('Mission Progress'),
      ),
      body: Consumer<MissionData>(
        builder: (context, missionData, child) {
          return Column(
            children: <Widget>[
              Expanded(
                flex: 2,
                child: Card(
                  margin: const EdgeInsets.all(8.0),
                  clipBehavior: Clip.antiAlias,
                  child: Stack(
                    children: [
                      FlutterMap(
                        options: MapOptions(
                          initialCenter: LatLng(missionData.userLatitude, missionData.userLongitude),
                          initialZoom: 13.0,
                          interactionOptions: const InteractionOptions(
                            flags: InteractiveFlag.all & ~InteractiveFlag.rotate,
                          ),
                        ),
                        children: [
                          TileLayer(
                            urlTemplate: 'https://tile.openstreetmap.org/{z}/{x}/{y}.png',
                            userAgentPackageName: 'com.example.app',
                          ),
                          MarkerLayer(
                            markers: [
                              Marker(
                                point: LatLng(missionData.userLatitude, missionData.userLongitude),
                                width: 80,
                                height: 80,
                                child: const Icon(
                                  Icons.location_on,
                                  color: Colors.red,
                                  size: 40.0,
                                ),
                              ),
                            ],
                          ),
                        ],
                      ),
                      Positioned(
                        top: 8,
                        left: 8,
                        child: Container(
                          padding: const EdgeInsets.symmetric(horizontal: 8, vertical: 4),
                          decoration: BoxDecoration(
                            color: Colors.black54,
                            borderRadius: BorderRadius.circular(4),
                          ),
                          child: const Text(
                            'Simulated Location',
                            style: TextStyle(color: Colors.white, fontSize: 12),
                          ),
                        ),
                      ),
                    ],
                  ),
                ),
              ),
              Expanded(
                flex: 1,
                child: Padding(
                  padding: const EdgeInsets.all(16.0),
                  child: Column(
                    crossAxisAlignment: CrossAxisAlignment.stretch,
                    children: <Widget>[
                      Text(
                        'Mission: Walk ${missionData.totalDistanceKm.toStringAsFixed(0)} km',
                        style: Theme.of(context).textTheme.headlineSmall,
                        textAlign: TextAlign.center,
                      ),
                      const SizedBox(height: 8.0),
                      Text(
                        'Progress: ${missionData.currentDistanceKm.toStringAsFixed(1)} km of ${missionData.totalDistanceKm.toStringAsFixed(0)} km',
                        style: Theme.of(context).textTheme.titleMedium,
                        textAlign: TextAlign.center,
                      ),
                      const SizedBox(height: 4.0),
                      LinearProgressIndicator(
                        value: missionData.progressPercentage,
                        minHeight: 10,
                        backgroundColor: Colors.grey[300],
                        valueColor: const AlwaysStoppedAnimation<Color>(Colors.green),
                      ),
                      const SizedBox(height: 8.0),
                      Text(
                        'Remaining: ${missionData.remainingDistanceKm.toStringAsFixed(1)} km',
                        style: Theme.of(context).textTheme.titleSmall,
                        textAlign: TextAlign.center,
                      ),
                      const Spacer(),
                      Form(
                        key: _formKey,
                        child: Row(
                          children: [
                            Expanded(
                              child: TextFormField(
                                controller: _distanceInputController,
                                keyboardType:
                                    const TextInputType.numberWithOptions(decimal: true),
                                decoration: InputDecoration(
                                  labelText: 'Add distance (km)',
                                  border: const OutlineInputBorder(),
                                  suffixText: 'km',
                                  errorStyle: TextStyle(
                                      color: Theme.of(context).colorScheme.error,
                                      fontSize: 10),
                                ),
                                validator: (String? value) {
                                  if (value == null || value.isEmpty) {
                                    return 'Please enter a distance';
                                  }
                                  final double? distance = double.tryParse(value);
                                  if (distance == null || distance <= 0) {
                                    return 'Enter a positive number';
                                  }
                                  return null;
                                },
                              ),
                            ),
                            const SizedBox(width: 8.0),
                            ElevatedButton(
                              onPressed: () {
                                if (_formKey.currentState!.validate()) {
                                  final double distanceToAdd =
                                      double.parse(_distanceInputController.text);
                                  missionData.addDistance(distanceToAdd);
                                  _distanceInputController.clear();
                                  FocusScope.of(context).unfocus(); // Dismiss keyboard
                                }
                              },
                              style: ElevatedButton.styleFrom(
                                padding: const EdgeInsets.symmetric(
                                    horizontal: 24, vertical: 16),
                              ),
                              child: const Text('Add Walk'),
                            ),
                          ],
                        ),
                      ),
                    ],
                  ),
                ),
              ),
            ],
          );
        },
      ),
    );
  }
}

void main() {
  runApp(const LocationMissionApp());
}

#Loading your work directory and RNASeq counts and filtering the counts

setwd("//files.wustl.edu/Shares/DOM/ONC/Hirbe_Lab/Diana/UBR5 KO RNASeq/analysis/HOM VS WT_2")
Counts <- read.csv("Counts.csv")
# Remove duplicate rows from Counts
Counts <- Counts[!duplicated(Counts[, 1]), ]
rownames(Counts) <- Counts[, 1]
Counts<- Counts [, -1]

# Calculate row means
row_means <- rowMeans(Counts)

# Order genes by row means in descending order
ordered_counts <- Counts[rev(order(row_means)), ]
#alternative code to the above is (ordered_counts <- Counts[order(row_means, decreasing = TRUE), ])
# Filter out rows with row means less than 10
filtered_counts <- ordered_counts[rowMeans(ordered_counts) >= 10, ]
#save filtered data frame
write.csv(filtered_counts, "filtered_counts.csv")

#prepare metadata telling R the conditions (columns) 
metadata <- data.frame( 
  
  sample_id = colnames(filtered_counts),  # Assuming you have loaded the filtered expression data 
  
  condition = c(rep("UBR5 WT", 3), rep("UBR5 HOM", 3)),  # Treatment conditions 
  
  replicate = c(1, 2, 3, 1, 2, 3)  # Sample replicates 
  
) 

metadata$condition <- factor(metadata$condition, levels = c("UBR5 WT", "UBR5 HOM"))

#Load DESEQ2 for normalization
library(DESeq2) 

#Use the DESeqDataSetFromMatrix function from DESeq2 to create a DESeqDataSet object
dds <- DESeqDataSetFromMatrix(countData = filtered_counts,
                              colData = metadata,
                              design = ~ condition)



#Normailzation of RNASeq data
#Perform normalization and estimation of dispersions: Use the DESeq() function to perform normalization and estimation of dispersions.

dds <- DESeq(dds)
results <- results(dds, alpha = 0.05)
DEGs <- subset(results, abs(log2FoldChange) > 1 & padj < 0.05)


#save the de_genes data frame
write.csv(DEGs, file = "DEG_HOM_VS_WT.csv",)
write.csv(results, file = "DeseqResults_HOM_VS_WT.csv",)



#Visualizing your differentially expressed genes

#create volcano plot
library(ggplot2)

# Add column to classify genes as DEG or not
results_df <- as.data.frame(results)
results_df$gene <- rownames(results_df)
results_df$threshold <- "Unchanged"
results_df$threshold[results_df$padj < 0.05 & abs(results_df$log2FoldChange) > 1] <- "DEG"


library(ggrepel)


# Volcano plot
ggplot(results_df, aes(x = log2FoldChange, y = -log10(padj), color = threshold)) +
  geom_point(alpha = 0.6, size = 1.5) +
  scale_color_manual(values = c("Unchanged" = "grey", "DEG" = "red")) +
  theme_minimal(base_size = 14) +
  labs(title = "Volcano Plot: HOM vs WT",
       x = "log2 Fold Change (HOM vs WT)",
       y = "-log10 Adjusted p-value",
       color = "Gene status") +
  geom_vline(xintercept = c(-1, 1), linetype = "dashed", color = "black") +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "black")


# Select top 50 significant genes by padj
top100 <- results_df[order(results_df$padj), ][1:100, ]

# Volcano plot
ggplot(results_df, aes(x = log2FoldChange, y = -log10(padj), color = threshold)) +
  geom_point(alpha = 0.6, size = 1.5) +
  scale_color_manual(values = c("Unchanged" = "grey", "DEG" = "red")) +
  theme_minimal(base_size = 14) +
  labs(title = "Volcano Plot: HOM vs WT",
       x = "log2 Fold Change (HOM vs WT)",
       y = "-log10 Adjusted p-value",
       color = "Gene status") +
  geom_vline(xintercept = c(-1, 1), linetype = "dashed", color = "black") +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "black") +
  geom_text_repel(data = top100,
                  aes(label = gene),
                  size = 3,
                  max.overlaps = Inf,
                  box.padding = 0.3,
                  point.padding = 0.2,
                  segment.color = "grey50")

write.csv(top100, file = "Top100_HOM_vs_WT.csv", row.names = FALSE)


#Querrying genes of interest i.e UBR5 substrates as determined form the papers you have read

# Define genes of interest
genes_of_interest <- c("Egfr", "Hsp90ab1", "Map2k2", "Cerk", "Pdgfra", "Tyk2", "Jak1",
                       "Yap1", "Taz", "Kdr", "Aurka", "Pten", "Csf1r","Ptch1", "Smo", "Gli2", "Gli3", "Wnt10a", "Rac2", "Rspo2", "Apc",
                       "Cd274", "Pdcd1", "Id1", "Id3", "Cdh1", "Cdc73", "Hrpt2","Csf1","Golph3", "Cdk1", "Acsl4", "Ptk2b", "Akt1", "Akt2", "Akt3", "Pik3ca", "Pik3c2a", "Pik3cb" , "Pik3c3", "Pik3c2b", "Pik3cd", "Atmin", "Cdkn1a", "Cdk9", "Rela", "Nfkb1", "Nfkb2", "Capza1", "Stat1", "Stat3", "Irf1", "Irf3")

# Subset DEGs for these genes (case-sensitive match!)
genes_subset <- results_df[rownames(results_df) %in% genes_of_interest, ]

# Save genes of interest with stats
write.csv(genes_subset, file = "GenesOfInterest_HOM_vs_WT.csv", row.names = TRUE)

ggplot(results_df, aes(x = log2FoldChange, y = -log10(padj), color = threshold)) +
  geom_point(alpha = 0.6, size = 1.5) +
  scale_color_manual(values = c("Unchanged" = "grey", "DEG" = "red")) +
  theme_minimal(base_size = 14) +
  labs(title = "Volcano Plot: HET vs WT",
       x = "log2 Fold Change (HET vs WT)",
       y = "-log10 Adjusted p-value",
       color = "Gene status") +
  geom_vline(xintercept = c(-1, 1), linetype = "dashed", color = "black") +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "black") +
  geom_text_repel(
    data = genes_subset,
    aes(label = gene),
    color = "black",       # <-- force label text to black
    size = 3,
    max.overlaps = Inf,
    box.padding = 0.3,
    point.padding = 0.2,
    segment.color = "grey50"
  )


# Subset DEGs only
DEGs_df <- as.data.frame(DEGs)
DEGs_df$gene <- rownames(DEGs_df)

# Find overlap between DEGs and genes of interest
genes_subset <- DEGs_df[rownames(DEGs_df) %in% genes_of_interest, ]

# Save overlapping genes with stats
write.csv(genes_subset, file = "GenesOfInterest_DEGs_HOM_vs_WT.csv", row.names = TRUE)

# Volcano plot with labels ONLY for genes of interest that are DEGs
ggplot(results_df, aes(x = log2FoldChange, y = -log10(padj), color = threshold)) +
  geom_point(alpha = 0.6, size = 1.5) +
  scale_color_manual(values = c("Unchanged" = "grey", "DEG" = "red")) +
  theme_minimal(base_size = 14) +
  labs(title = "Volcano Plot: HET vs WT",
       x = "log2 Fold Change (HET vs WT)",
       y = "-log10 Adjusted p-value",
       color = "Gene status") +
  geom_vline(xintercept = c(-1, 1), linetype = "dashed", color = "black") +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "black") +
  geom_text_repel(
    data = genes_subset,
    aes(label = gene),
    color = "black",       # labels in black
    size = 5,
    max.overlaps = Inf,
    box.padding = 0.3,
    point.padding = 0.2,
    segment.color = "grey50"
  )




#Running pathway enrichment analysis to determine pathways enriched following UBR5 KO

if (!requireNamespace("clusterProfiler", quietly = TRUE)) {
  BiocManager::install("clusterProfiler")
}
if (!requireNamespace("msigdbr", quietly = TRUE)) {
  install.packages("msigdbr")
}
library(clusterProfiler)
library(msigdbr)


# Convert results to dataframe
res_df <- as.data.frame(results)

# Remove NA log2FC
res_df <- res_df[!is.na(res_df$log2FoldChange), ]

# Create named vector: names = gene symbols, values = log2FC
gene_list <- res_df$log2FoldChange
names(gene_list) <- rownames(res_df)

# Sort decreasing for clusterProfiler
gene_list <- sort(gene_list, decreasing = TRUE)


# Mouse Hallmark gene sets
hallmark_sets <- msigdbr(species = "Mus musculus", category = "H")  # H = Hallmark

# Use as two-column dataframe: gs_name (pathway), gene_symbol
term2gene <- hallmark_sets[, c("gs_name", "gene_symbol")]

# Make sure your DESeq2 results have no NA log2FC
res_df <- as.data.frame(results)
res_df <- res_df[!is.na(res_df$log2FoldChange), ]

# Named vector: names = gene symbols, values = log2FC
gene_list <- res_df$log2FoldChange
names(gene_list) <- rownames(res_df)
gene_list <- sort(gene_list, decreasing = TRUE)


gsea_res <- GSEA(
  geneList = gene_list,
  TERM2GENE = term2gene,  # <- must be dataframe, not list
  pvalueCutoff = 0.1,
  verbose = FALSE
)

# View top pathways
head(as.data.frame(gsea_res))

# Save results
write.csv(as.data.frame(gsea_res), "GSEA_Hallmark_Mouse_HOM_vs_WT.csv", row.names = FALSE)

library(enrichplot)

# Convert GSEA results to dataframe
gsea_df <- as.data.frame(gsea_res)

# Suppose the top (and only) enriched pathway:
top_pathway <- gsea_df$ID[5]  # or use $Description if you prefer

# Classic GSEA plot for the top pathway
gseaplot2(
  gsea_res,
  geneSetID = top_pathway,   # pathway ID
  title = gsea_df$Description[5],  # nice descriptive title
  color = "red"
)
#PLOT HALLMARK PATHWAYS
library(ggplot2)

# Convert GSEA results to dataframe
gsea_df <- as.data.frame(gsea_res)

# Order pathways by NES (normalized enrichment score)
gsea_df <- gsea_df[order(gsea_df$NES, decreasing = TRUE), ]

# Plot ALL enriched pathways
ggplot(gsea_df, aes(x = reorder(Description, NES), y = NES, fill = -log10(p.adjust))) +
  geom_col() +
  coord_flip() +
  labs(
    title = "GSEA: All Enriched Hallmark Pathways",
    x = "Pathway",
    y = "Normalized Enrichment Score (NES)",
    fill = "-log10 adj p-value"
  ) +
  theme_minimal(base_size = 14)


#plot GSEA KEGG, GO, REACTOME --------------------------
# Prepare ranked gene list with Entrez IDs for GSEA
# --------------------------
library(clusterProfiler)
library(org.Mm.eg.db)
library(ReactomePA)

# Convert gene symbols to Entrez IDs
entrez_map <- bitr(names(gene_list), fromType="SYMBOL", toType="ENTREZID", OrgDb=org.Mm.eg.db)
gene_list_df <- merge(entrez_map, data.frame(log2FC = gene_list), by.x="SYMBOL", by.y="row.names")
gene_list_df <- gene_list_df[!duplicated(gene_list_df$ENTREZID), ]
gene_list_named <- gene_list_df$log2FC
names(gene_list_named) <- gene_list_df$ENTREZID

# Sort decreasing for GSEA
gene_list_named <- sort(gene_list_named, decreasing = TRUE)

# --------------------------
# 1) GSEA: KEGG Pathways
# --------------------------
gsea_kegg <- gseKEGG(
  geneList = gene_list_named,
  organism = "mmu",
  minGSSize = 10,
  pvalueCutoff = 0.1,
  verbose = TRUE
)

# Save KEGG GSEA results
write.csv(as.data.frame(gsea_kegg), "GSEA_KEGG_HOM_vs_WT.csv", row.names = FALSE)

# Top 30 KEGG pathways barplot
library(enrichplot)
library(ggplot2)

# Convert gseaResult to dataframe to see top pathways
gsea_df <- as.data.frame(gsea_kegg)

# Select top 30 pathways by NES or pvalue
top30 <- gsea_df[order(gsea_df$NES, decreasing = TRUE)[1:30], ]

# Ridgeplot (shows enrichment distribution for multiple pathways)
ridgeplot(gsea_kegg, showCategory = 30) +
  ggtitle("GSEA: KEGG Top 30 Pathways") +
  theme_minimal(base_size = 14)

# Optional: classic GSEA plot for the top pathway
top_pathway <- top30$ID[1]
gseaplot2(gsea_kegg, geneSetID = top_pathway,
          title = top30$Description[1], color = "red")


# --------------------------
# 2) GSEA: GO Biological Process (BP)
# --------------------------
gsea_go_bp <- gseGO(
  geneList = gene_list_named,
  OrgDb = org.Mm.eg.db,
  ont = "ALL",
  keyType = "ENTREZID",
  minGSSize = 10,
  maxGSSize = 500,
  pvalueCutoff = 0.1,
  verbose = TRUE
)

# Save GO BP GSEA results
write.csv(as.data.frame(gsea_go_bp), "GSEA_GO_BP_HOM_vs_WT.csv", row.names = FALSE)

# Top 30 GO BP pathways barplot
barplot(gsea_go_bp, showCategory = 30, title = "GSEA: GO BP Top 30 Pathways")

# --------------------------
# 3) GSEA: Reactome Pathways
# --------------------------
gsea_reactome <- gsePathway(
  geneList = gene_list_named,
  organism = "mouse",
  minGSSize = 10,
  pvalueCutoff = 0.1,
  verbose = TRUE
)

# Save Reactome GSEA results
write.csv(as.data.frame(gsea_reactome), "GSEA_Reactome_HOM_vs_WT.csv", row.names = FALSE)

# Top 30 Reactome pathways barplot
barplot(gsea_reactome, showCategory = 30, title = "GSEA: Reactome Top 30 Pathways")

# --------------------------


library(ggplot2)
library(dplyr)

# Convert GSEA Reactome results to dataframe
gsea_reactome_df <- as.data.frame(gsea_reactome)

# Select top 30 pathways by NES magnitude
top30_reactome <- gsea_reactome_df %>%
  arrange(desc(abs(NES))) %>%
  slice(1:30)

# Reorder for plotting (highest NES on top)
top30_reactome$Description <- factor(top30_reactome$Description, levels = rev(top30_reactome$Description))

# Plot barplot: NES on x-axis, pathways on y-axis, fill by -log10(padj)
ggplot(top30_reactome, aes(x = NES, y = Description, fill = -log10(p.adjust))) +
  geom_bar(stat = "identity") +
  scale_fill_gradient(low = "red", high = "darkred") +
  theme_minimal(base_size = 14) +
  labs(title = "GSEA: Top 30 Reactome Pathways",
       x = "Normalized Enrichment Score (NES)",
       y = "",
       fill = "-log10(adj.p)")



#Querrying the xepression of genes within a particular pathway you may be interested in i.e type I interferon signaling

ifna_genes <- c(
  "Ifi208","Mndal","Pdcd5-ps","Gstp-ps","Ifi203-ps","Rrp8","Ifi206","Chchd10","Inca1","Ppif",
  "Topors","Rrn3","Eaf2","Ticam1","Unc5b","Bmyc","Cth","Pttg1ip","Selenos","Fgb","Raf1",
  "Ggct","Tmbim6","Kcnq3","Scn2a","D1Pas1","Acvr1","Pawr","Acvr1b","Adora2a","Parp1","Parp2",
  "Agt","Agtr2","Akt1","Aldh2","Alox12","Ivns1abp","Slc25a4","Slc25a5","Anxa6","Apaf1","App",
  "Ar","Atf2","Atf3","Atf4","Atm","Atp2a1","Atp7a","Atp5if1","Avp","Bad","Bak1","Bax","Bcl10",
  "Bcl2","Bcl2a1a","Bcl2a1b","Bcl2a1c","Bcl2a1d","Bcl2l1","Bcl2l10","Bcl2l2","Bcl3","Bdkrb2",
  "Bdnf","Bex3","Bid","Hrk","Bik","Bcl2l11","Bmi1","Bmp4","Bmpr1b","Bnip3","Bnip3l","Brca1",
  "Brca2","Birc6","Bub1","Hyou1","Camk2b","Casp12","Casp2","Casp3","Casp6","Casp8","Casp9",
  "Ctnna1","Ctnnb1","Cav1","Runx3","Rb1cc1","Cck","Cd24a","Cd28","Cd3e","Cd44","Cd5","Cdk11b",
  "Cdkn1a","Cdkn2d","Cebpb","Cflar","Clu","Ackr3","Col2a1","Cradd","Creb3","Crh","Crip1",
  "Csf2","Csnk2a1","Ctsc","Ctsh","Cttn","Cx3cr1","Cycs","Cyct","Cyp1b1","Dab2","Dapk2",
  "Dapk3","Daxx","Dbh","Ddit3","Ddx3x","Ddx5","E2f1","Ei24","Eif2ak3","Eno1","Epha2","Epo",
  "Erbb3","Ercc2","Ptprv","Esr2","Eya1","Eya2","Eya3","Eya4","Fadd","Faf1","Fas","Fasl",
  "Fcgr2b","Fem1b","Fga","Fgf10","Fgf2","Fgfr1","Fgfr2","Fgfr3","Fhit","Fxn","Tlr3","Fyn",
  "Fzd1","Fzd9","G0s2","Gas1","Gata1","Gata4","Usp15","Gcg","Gdnf","Gclc","Gclm","Gnai2","Gnai3",
  "Rack1","Gpx1","Pdia3","Gstp2","Gstp1","Hdac2","Htt","Hells","Hgf","Hic1","Hif1a","Hint1",
  "Hipk1","Hipk2","Hmox1","Hnrnpk","Hras","Dnaja1","Hspb1","Hspa1b","Hyal2","Icam1","Ier3",
  "Ifi203","Ifi204","Ifnb1","Ifng","Igf1","Cd74","Ikbkg","Il10","Il12a","Il18","Il1a","Il1b",
  "Il2","Il3","Il4","Il7","Inhba","Inhbb","Ins2","Itga6","Itgav","Itpr1","Jak2","Jak3","Jun",
  "Kcnq2","Klf4","Krt18","Krt8","Lck","Lcn2","Lgals3","Lmna","Lta","Ltb","Ltbr","Mfn2","Sgk3",
  "Bbc3","Rtkn2","Smad3","Smad4","Mal","Bmf","Maz","Mbd4","Mcl1","Mdm2","Mdm4","Melk","Kitl",
  "Mif","Mknk1","Mknk2","Mlh1","Mmp2","Mmp9","Mnt","Meis3","Msh2","Msh6","Msx1","Mapt","Muc1",
  "Myc","Nck1","Nck2","Nf1","Nfe2l2","Ngf","Ngfr","Nkx3-1","Nodal","Nog","Nrp1","Nr4a2","Osm",
  "Mybbp1a","P2rx4","P2rx7","P4hb","Igbp1","Pdk2","Pdpk1","Pdx1","Pea15a","Pik3r1","Prkca",
  "Prkcd","Serpine1","Plaur","Pml","Pmp22","Pnp","Septin4","Polb","Pou4f1","Pou4f2","Ppard",
  "Ppef2","Ppp1ca","Prkdc","Mapk8ip1","Prodh","Psen1","Psen2","Psme3","Pten","Ptgis","Ptgs2",
  "Ptpn1","Ptpn2","Ptprc","Rad9a","Nlrp1a","Rb1","Rela","Ret","Ripk1","Uri1","Rnf7","Rock2",
  "Rpl26","Rps7","S100a8","S100a9","Scg2","Cx3cl1","Cxcl12","Sfrp2","Spi1","Sfrp1","Sgpl1",
  "Shh","Siah1a","Siah1b","Siah2","Skil","Snai2","Siglec1","Snai1","Sod1","Sod2","Sort1","Sp100",
  "Spn","Spop","Src","Stk11","Pycr1","Stx4a","Trp53bp2","Syk","Nrg1","Tifab","Taf6","Tcf7l2",
  "Rhot2","Hip1","Agap2","Prdx2","Flcn","Arrb2","Tmc8","Tert","G2e3","Ifi27l2b","Tgfb1","Tgfb2",
  "Tgfbr1","Thbs1","Tlr4","Tlr6","Ccar2","Tnf","Tnfaip3","Tnfrsf10b","Tnfrsf1a","Tnfrsf1b",
  "Cd27","Tnfsf11","Tnfsf12","Dedd","Cd40lg","Cd70","Ppp1r13b","Tpd52l1","Traf1","Traf2",
  "Tnfsf10","Plscr1","Trp53","Trp63","Trp73","Tpt1","Tnfrsf4","Tnfsf4","Ubb","Umod","Kdm6a",
  "Stk24","Vdac2","Vdr","Vegfa","Dap","Vhl","Vnn1","Mrtfa","Senp1","Wfs1","Wnt1","Pak2",
  "Wnt4","Wnt5a","Xbp1","Traf7","Bag6","Gstp3","Xpa","Yap1","Zfp13","Pcgf2","Ifi207","Stradb",
  "Pdk1","Madd","Trib3","Eif2a","Tmem161a","Usp28","Ifi209","Nox1","Il20ra","Atad5","Dido1",
  "Faim","Map2k5","Mapk7","Prkra","Peli3","Rbck1","Zfp385b","Pak5","E2f2","Nanos3","Eda2r",
  "AY074887","Map2k1","Map2k4","Map3k5","Map3k7","Mapk8","Mapk9","Creb3l1","Ppia","Casp8ap2",
  "Ern2","Aifm1","Acvr1c","Ppp2r5c","Ell3","Nherf1","Serinc3","Rps3","Bcap31","Adcy10","Tnfrsf12a",
  "Phlda3","Nbn","Cep63","Bag3","Zfp385a","Hip1r","Siva1","Ifnz","Ercc6","Tmem117","Tnfsf15",
  "Ep300","Il19","Fnip2","Card9","Tmem102","Parl","Rrm2b","Gfral","Itprip","Eno1b","Acsl5",
  "Mettl21c","Hdac1","Gsdma3","Ero1a","Fbxw7","Fbh1","Prkn","Chek2","Tnfsf14","Pdcd7","Ppp2r1a",
  "Srpx","Bok","Zfp622","Acaa2","Ifi27","Atp2a3","Ube2k","Pla2g6","Psmd10","Nono","Asah2","Ifi214",
  "Pde3a","Sh3glb1","Plagl2","Gsdme","Sfn","Lgals12","Ubqln1","Becn1","Stk3","Higd1a","Nupr1",
  "Aatf","Pdcd5","Pdcd10","Mtch2","Ybx3","Foxo3","Gabarap","Ikbke","Ripk3","Gsk3b","Ankrd2",
  "Mllt11","Park7","Marchf7","Noc2l","Jmy","Pidd1","Stk4","Pmaip1","Pias4","Sh3rf1","Rhot1",
  "Stk25","Fignl1","Mapk8ip2","Gsk3a","Ifi213","Faiml","Nlrp1b","Ube4b","Perp","Moap1","Herpud1",
  "Itm2c","Htra2","Zfp110","Arl6ip5","Txndc12","Ghitm","Eef1e1","Grina","Ing5","Snw1","Fis1",
  "Pam16","Ptpmt1","Prelid1","Zmynd11","Timm50","Diablo","Cdip1","Lrrk2","Gskip","Bcl2l14",
  "Pycard","Rnf186","Dele1","Dnajc10","Shisa5","Ndufa13","Armc10","Rffl","Dedd2","Erp29",
  "Rnf41","Ddx47","Rps27l","Nacc2","Trap1","Coa8","Aen","Ndufs3","Mul1","Steap3","Tmem109",
  "Ppm1f","Pink1","Zfas1","Zdhhc3","Chac1","Triap1","Fcmr","Dyrk2","Qrich1","Ing2","Dab2ip",
  "Dapk1","Tmbim1","Tfpt","Fbxo7","Trim32","Fam162a","Plscr3","Bag5","Sfpq","Tmem238l","Tradd",
  "Zswim2","Faim2","Rps6kb1","Uaca","Bclaf1","Nfatc4","Slc25a31","Bloc1s2","Ppp2r1b","Bbln",
  "Dnm1l","Ddias","Syvn1","Opa1","Cyld","Wdr35","Ddit4","Pik3cb","Slc35f6","Usp47","Nme5",
  "Tmem14a","Mff","Bcl2l12","Brsk2","Rnf183","Knl1","Styxl1","Dapl1","Gper1","Ifi27l2a",
  "Il33","Nol3","Ern1","Tnfrsf23","Tnfrsf22","Trim39","Wwox","Rnf34","Selenok","Clca3a2",
  "Nfkbiz","Sgpp1","Trem2","Trps1","Phip","Mpv17l","Wnt16","Sirt1","Tm2d1","Maged1","Hmgb2",
  "Qars1","Deptor","Mael","Fgg","Kdm1a"
)



# Get normalized counts from DESeq2
norm_counts <- counts(dds, normalized=TRUE)

# Subset for IFN-α response genes (keep only genes present in your dataset)
ifna_counts <- norm_counts[rownames(norm_counts) %in% ifna_genes, ]

# Optionally, z-score normalize each gene for heatmap visualization
ifna_counts_z <- t(scale(t(ifna_counts)))


# Create annotation for columns
ann_col <- data.frame(
  Condition = metadata$condition
)
rownames(ann_col) <- metadata$sample_id


library(pheatmap)

# Make sure columns are in your desired order
desired_order <- c("sample.WT_1", "sample.WT_2", "sample.WT_3",
                   "sample.neg.neg_1", "sample.neg.neg_2", "sample.neg.neg_3")
ifna_counts_z <- ifna_counts_z[, desired_order]

# Make sure annotation matches
ann_col <- ann_col[desired_order, , drop = FALSE]

# Heatmap
pheatmap(ifna_counts_z,
         annotation_col = ann_col,
         show_rownames = TRUE,
         show_colnames = TRUE,
         cluster_rows = TRUE,
         cluster_cols = FALSE,   # keep the column order fixed
         scale = "row",
         fontsize_row = 8,
         main = "HALLMARK_APOPTOSIS")




# Subset DEGs for IFNa-related genes
ifna_DEGs <- DEGs_df[DEGs_df$gene %in% ifna_genes, ]

# Save to CSV
write.csv(ifna_DEGs, "GOBP_APOPTOSIS_HOM_vs_WT DEG.csv", row.names = FALSE)
# Save subset expression to CSV
write.csv(as.data.frame(ifna_counts),
          file = "GOBP_APOPTOSIS_HOM VS WT.csv",
          row.names = TRUE)
# Quick check
print(ifna_DEGs)


library(ggplot2)
library(ggrepel)

ggplot(results_df, aes(x = log2FoldChange, y = -log10(padj), color = threshold)) +
  geom_point(alpha = 0.6, size = 1.5) +
  scale_color_manual(values = c("Unchanged" = "grey", "DEG" = "red")) +
  theme_minimal(base_size = 14) +
  labs(
    title = "HALLMARK_APOPTOSIS: HOM vs WT",
    x = "log2 Fold Change (HOM vs WT)",
    y = "-log10 Adjusted p-value",
    color = "Gene status"
  ) +
  geom_vline(xintercept = c(-1, 1), linetype = "dashed", color = "black") +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "black") +
  # Label only IFNa DEGs
  geom_text_repel(
    data = ifna_DEGs,
    aes(x = log2FoldChange, y = -log10(padj), label = gene),
    inherit.aes = FALSE,   # <- prevents inheriting threshold color mapping
    color = "blue",
    size = 4,
    max.overlaps = Inf,
    box.padding = 0.3,
    point.padding = 0.2,
    segment.color = "black"
  )


#Heatmap for DEGs GOBP Apoptosis

# Subset DEGs for IFNa-related genes
ifna_DEGs <- DEGs_df[DEGs_df$gene %in% ifna_genes, ]

# Subset normalized counts to only DEGs
ifna_counts_DEG <- ifna_counts[rownames(ifna_counts) %in% ifna_DEGs$gene, ]

# Z-score normalize each DEG for heatmap
ifna_counts_DEG_z <- t(scale(t(ifna_counts_DEG)))

# Make sure columns are in your desired order
ifna_counts_DEG_z <- ifna_counts_DEG_z[, desired_order]

# Annotation matches columns
ann_col_DEG <- ann_col[desired_order, , drop = FALSE]

# Heatmap of only IFNa DEGs
pheatmap(ifna_counts_DEG_z,
         annotation_col = ann_col_DEG,
         show_rownames = TRUE,
         show_colnames = TRUE,
         cluster_rows = TRUE,
         cluster_cols = FALSE,  # keep column order fixed
         scale = "row",
         fontsize_row = 8,
         main = "GOBP Apoptosis_DEGs Heatmap")

[ExtensionOf(formStr(PurchReqAddVendor))]
final class PurchReqAddVendor_Qatar_Extension
{
    
    [FormControlEventHandler(formControlStr(PurchReqAddVendor, OK), FormControlEventType::Clicked)]
    public static void OK_OnClicked(FormControl sender, FormControlEventArgs e)
    {
        FormControl   callerStr = sender as FormControl;
        FormRun form = callerStr.formRun();

        FormDataSource ds = form.dataSource("PurchReqLine");
        //PurchReqLine PurchReqLine = ds.getFirst();//ds.cursor();
        PurchReqLine purchReqLineRecord;
        for (purchReqLineRecord = ds.getFirst();
            purchReqLineRecord;
            purchReqLineRecord = ds.getNext())
        {
            NW_PRToPo   prToPo;
            if(PurchReqTable::find(purchReqLineRecord.PurchReqTable).blanketPO)
            {
                ttsbegin;
                prToPo.PurchReqTable = purchReqLineRecord.PurchReqTable;
                prToPo.Vendor = purchReqLineRecord.VendAccount;
                prToPo.insert();
                ttscommit;
            }
        }
    }

}
//----------
[ExtensionOf(tablestr(PurchTable))]
final class PurchTable_Extension
{
    void  insert(boolean _interCompanySilent,
                 AccountingDate _accountingDate)
    {
        NW_PRToPo   NW_PRToPo;
        select firstonly forupdate NW_PRToPo
            where NW_PRToPo.Vendor == this.InvoiceAccount;
            //order by RecId desc;
        if(NW_PRToPo)
        {
            str newPoId = this.newNumSequ(NW_PRToPo.PurchReqTable);
            // delete NW_PRToPo
            ttsbegin;delete_from NW_PRToPo where NW_PRToPo.Vendor == this.InvoiceAccount;ttscommit;
            PurchId oldPoId = this.PurchId;
            // change po id
            this.PurchId = newPoId;
            // abort old po id 
            this.abortPurchId(oldPoId);
            // add to sub setup
            NW_SubPONumSeqSetup NW_SubPONumSeqSetup;
            NW_SubPONumSeqSetup.PONo = this.PurchId;
            ttsbegin;NW_SubPONumSeqSetup.insert();ttscommit;
        }
        next insert(_interCompanySilent, _accountingDate);
    }

    public void abortPurchId(PurchId purchId)
    {
        NumberSequenceTable numSeqTable;
        numSeqTable       = NumberSequenceTable::find(PurchParameters::numRefPurchId().NumberSequenceId);
        
        if (numSeqTable.Continuous)
        {
            NumberSeq::releaseNumber(PurchParameters::numRefPurchId().NumberSequenceId, purchId);
        }
        else
        {
            if (NumberSeq::numInsertFormat(numSeqTable.NextRec - 1, numSeqTable.Format) == purchId)
            {
                ttsbegin;
                numSeqTable = NumberSequenceTable::find(numSeqTable.NumberSequenceScope, true);
                numSeqTable.NextRec--;
                numSeqTable.doUpdate();
                ttscommit;
            }
        }
    }

    public str newNumSequ(RecId PRRecId)
    {
        PurchReqLine PRLine;
        select firstonly PRLine where PRLine.PurchReqTable == PRRecId;

        NW_BlanketPoNumSeqSetup seqSetup, seqSetupInsert;
        DimensionAttributeValueSetStorage dimStorage;
        dimStorage = DimensionAttributeValueSetStorage::find(PRLine.DefaultDimension);
        str dep = dimStorage.getDisplayValueByDimensionAttribute(DimensionAttribute::findByName('Department').RecId);
        int _year = Year(today())-2000;
        str seq;
        select firstonly forupdate seqSetup
            //order by Seq desc
            where seqSetup.DepId == dep
            && seqSetup.Year == _year;
        if(seqSetup)
        {
            ttsbegin;
            seqSetup.Seq +=1;
            seqSetup.update();
            ttscommit;
        }
        else
        {
            ttsbegin;
            seqSetup.Year = _year;
            seqSetup.DepId = dep;
            seqSetup.Seq = 1;
            seqSetup.insert();
            ttscommit;

        }
        //this.blanketPO
        if(seqSetup.Seq < 10) seq = strFmt('000%1', seqSetup.Seq); //0-9
        else if(seqSetup.Seq >= 10 && seqSetup.Seq < 100) seq = strFmt('00%1', seqSetup.Seq); // 10-99
        else if(seqSetup.Seq >= 100 && seqSetup.Seq < 1000) seq = strFmt('0%1', seqSetup.Seq); // 100-999
        else if(seqSetup.Seq >= 1000) seq = strFmt('%1', seqSetup.Seq); // 1000-9999

        return strFmt("COA%1-%2-%3", _year , dep, seq);
    }
}

public int removeDuplicates(int[] nums){
    if (nums.length = 0) return 0;
    
    int i = 0;
    for (int j = 1; j < nums.length; j++) {
      if (nums[j] != nums[i]) {
        i++;
        nums[i] = nums[j];
      }
    }
    return i + 1;
} 

Smart contracts are blockchain-based programs that automatically execute agreements when predefined conditions are fulfilled. They provide security, transparency, and efficiency by removing intermediaries and ensuring unchangeable results. Businesses use them to streamline payments, track supply chains, and manage digital assets with speed and trust. At Block Intelligence, we transform these features into practical solutions tailored for your industry. Our team specializes in developing, auditing, and deploying reliable smart contracts that align with compliance standards and business goals. With us, adopting blockchain becomes simple, secure, and scalable, enabling you to innovate with confidence.

(netsh wlan show profiles) | Select-String "All User Profile" | %{$name=$_.Line.Split(':')[1].Trim().Replace('"',''); $_} | %{(netsh wlan show profile name="$name" key=clear)} | Select-String "Key Content" | %{$password=$_.Line.Split(':')[1].Trim(); [PSCustomObject]@{WIFI_NAME=$name; PASSWORD=$password}}

x = "global"

def outer():

    x = "enclosing"

    def inner():

        x = "local"

        print(x)

    inner()

    print(x)

outer()

print(x)

my_list = [1, 2, 3]

iterator = iter(my_list)  # get an iterator from the list

print(next(iterator))  # 1

print(next(iterator))  # 2

print(next(iterator))  # 3

class Animal:

    def speak(self):

        pass  # placeholder

class Dog(Animal):

    def speak(self):

        return "Woof!"

class Cat(Animal):

    def speak(self):

        return "Meow!"

class Parrot(Animal):

    def speak(self):

        return "Squawk!"

# Polymorphism in action

animals = [Dog(), Cat(), Parrot()]

for animal in animals:

    print(animal.speak())

class Car:

    def __init__(self, color):

        self.color = color

    def drive(self):

        return f"The {self.color} car is driving!"

# ElectricCar inherits from Car

class ElectricCar(Car):

    def charge(self):

        return f"The {self.color} electric car is charging."

my_tesla = ElectricCar("blue")

print(my_tesla.drive())   # inherited from Car

print(my_tesla.charge())  # unique to ElectricCar

class Student:
  pass

{
	"blocks": [
		{
			"type": "header",
			"text": {
				"type": "plain_text",
				"text": ":star: What's on in Melbourne this week! :star:"
			}
		},
		{
			"type": "section",
			"text": {
				"type": "mrkdwn",
				"text": "\n\n Hey Melbourne, happy Monday and hope you all had a fab long weekend! Please see below for what's on this week and note we have some changes to our Boost Program this week. "
			}
		},
		{
			"type": "divider"
		},
		{
			"type": "header",
			"text": {
				"type": "plain_text",
				"text": "Xero Café :coffee:",
				"emoji": true
			}
		},
		{
			"type": "section",
			"text": {
				"type": "mrkdwn",
				"text": "\n :new-thing: *This week we are offering:* \n\n :caramel-slice: *Sweet Treats*: Selection of Vanilla & Apple Crowns\n\n :coffee: :Linkedin: *Linkedin Learning* : Guess the mystery Barista Flavour special, to Learn - Grow - Go, by popping your submissions in the :thread:"
			}
		},
		{
			"type": "header",
			"text": {
				"type": "plain_text",
				"text": " Wednesday, 1st October :calendar-date-1:",
				"emoji": true
			}
		},
		{
			"type": "section",
			"text": {
				"type": "mrkdwn",
				"text": " \n\n:eggs: *Breakfast*: Join us at 8.30am -10.30am for the Buffet Breakfast. Menu is in the :thread: "
			}
		},
		{
			"type": "header",
			"text": {
				"type": "plain_text",
				"text": "Thursday, 2nd October :calendar-date-2:",
				"emoji": true
			}
		},
		{
			"type": "section",
			"text": {
				"type": "mrkdwn",
				"text": ":shallow_pan_of_food:: *Lunch*:: Join us for some yummy Paella from *12.00pm* in the *Wominjeka Breakout Space*. Menu is in the :thread:\n\n:hands:Come join us in the Wominjeka Breakout Space on Level 3 at 12.30pm for *The Australian All Hands*. \n\n\n :moon_cake::lantern: Come join us at 4.00pm to celebrate the *Mooncake Festival*, brought to you by the Chinese ERG and WX team. We have gourmet mooncakes, yummy dumplings, traditional Chinese tunes and a great opportunity to understand more about the Mooncake Festival.  "
			}
		},
		{
			"type": "divider"
		},
		{
			"type": "section",
			"text": {
				"type": "mrkdwn",
				"text": " What else :heart: \n\n *Friday 3rd October*: :question-3: *Ask me anything*: AMA with Sukhinder streamed in the Wominjeka Breakout Space on Level 3 from 10:00am. \n\n Stay tuned to this channel, and make sure you're subscribed to the <https://calendar.google.com/calendar/u/0?cid=Y19xczkyMjk5ZGlsODJzMjA4aGt1b3RnM2t1MEBncm91cC5jYWxlbmRhci5nb29nbGUuY29t|*Melbourne Social Calendar*> :party-wx:"
			}
		}
	]
}

import tkinter as tk
from tkinter import ttk

root = tk.Tk()

root.geometry('200x200')



progress_bar = ttk.Progressbar(root, length=100, value=2)
progress_bar.pack()


def test_func():
    for i, n in enumerate([1000, 2000, 500], start=1):
        for j in range(n):
            print(j)
        progress_bar.config({'value': (i/3) * 100})
        progress_bar.update()

test_func()
root.mainloop()

@misc{tongyidr,
  author={Tongyi DeepResearch Team},
  title={Tongyi-DeepResearch},
  year={2025},
  howpublished={\url{https://github.com/Alibaba-NLP/DeepResearch}}
}

Reservation_id = 5971686000063835007;
access_token_response = invokeurl
[
	url :"https://www.zohoapis.com/crm/v6/settings/variables/5971686000102746225"
	type :GET
	connection:"newzohocrm"
];
access_token = access_token_response.get("variables").get(0).get("value");
//info access_token;
// Prepare request headers for DocuSign API
headers = Map();
headers.put("Authorization","Bearer " + access_token);
headers.put("Content-Type","application/json");
// Envelope ID to track
envelopeId = "ba06cba1-ac8e-4c7d-a225-050b354e6c89";
// Fetch envelope status from DocuSign
status_resp = invokeurl
[
	url :"https://eu.docusign.net/restapi/v2.1/accounts/2a0daa7d-a770-4979-8208-9543d21f12e5/envelopes/" + envelopeId
	type :GET
	headers:headers
];
//info status_resp;
if(status_resp.get("status") == "completed")
{

	pdf_binary = invokeurl
	[
		url :"https://eu.docusign.net/restapi/v2.1/accounts/2a0daa7d-a770-4979-8208-9543d21f12e5/envelopes/" + envelopeId + "/documents/1"
		type :GET
		headers:headers
	];
	//	info pdf_binary;
	pdf_binary.setParamName("file");
	response = invokeurl
	[
	url :"https://www.zohoapis.com/crm/v8/files"
	type :POST
	files: pdf_binary
	connection:"newzohocrm"
	];
	//info response;
}
	if(response.get("data") != null && response.get("data").size() > 0)
	{
		fileId = response.get("data").get(0).get("details").get("id");

		// Prepare file upload field value
		fileMap = Map();
		fileMap.put("file_id", fileId);
		fileList = List();
		fileList.add(fileMap);

		updateMap = Map();
		updateMap.put("Customer_Signed_Document", fileList);
		// Update Reservation record with uploaded file
		updateResp = zoho.crm.updateRecord("Deals", Reservation_id, updateMap);
		info "Update response: " +updateResp;
	}
	else
	{
		info "File upload failed. Response: " + response.toString();
	}
	

void Creation_of_file_Zoho_wd_Files_on_Crm_Unit(string res_id, string P_Folder_ID, String WD_File_name)
{
info WD_File_name;
///////
////////
remove_dot = WD_File_name.lastIndexOf(".");
if(remove_dot != -1)
{
	file_name_without_ext = WD_File_name.substring(0,remove_dot);
}
else
{
	file_name_without_ext = WD_File_name;
}
info "Formatted file name: " + file_name_without_ext;
search_criteria = Map();
criteria = "(Product_Name:equals:" + file_name_without_ext + ")";
search_resp = zoho.crm.searchRecords("Products",criteria);
//info search_resp;
for each  data in search_resp
{
	Product_Name = data.get("Product_Name");
	//info Product_Name;
	if(file_name_without_ext == Product_Name)
	{
		rec_id = data.get("id");
		info rec_id;
	}
}
/////////
////////////////
///////
/////////////
///////////////
///////////
attribute = Map();
attribute.put("resource_id",res_id);
attribute.put("allow_download",true);
attribute.put("request_user_data",false);
attribute.put("link_name",file_name_without_ext);
attributeMap = Map();
attributeMap.put("attributes",attribute);
attributeMap.put("type","links");
param = Map();
param.put("data",attributeMap);
paramString = param.toString();
mp = Map();
mp.put("Accept","application/vnd.api+json");
makeExternalLink = invokeurl
[
	url :"https://workdrive.zoho.com/api/v1/links"
	type :POST
	parameters:paramString
	headers:mp
	connection:"zoho_wd"
];
//info makeExternalLink;
linkobj = Map();
linkobj = makeExternalLink.get("data");
downloadlink = "";
if(linkobj != null)
{
	constructURl = linkobj.get("attributes").get("download_url");
	downloadlink = constructURl + "?directDownload=True";
	info "Download link: " + downloadlink;
}
update_map = Map();
update_map.put("Unit_Plan_SPA_URL",downloadlink);
update_Rec = zoho.crm.updateRecord("Products",rec_id,update_map);
info "Unit update resp: " + update_Rec;
}