Mix

.gitignore

@@ -21,3 +21,22 @@ network/graph1_STRING_Magagnes20092default node.csv
 .idea/misc.xml
 .idea/Muscle_wasting.iml
 *.bkp
+*.sif
+network/Sessions/*
+*.png
+*.gif
+*.png
+network/.ipynb_checkpoints/*
+network/.ipynb_checkpoints/mirnas_influence_01-checkpoint.ipynb
+network/.ipynb_checkpoints/mirnas_influence_02-checkpoint.ipynb
+network/.ipynb_checkpoints/mirnas_influence_03_90-checkpoint.ipynb
+.virtual_documents/*
+network/data/inmune_genes_symbol.txt
+network/.virtual_documents/Untitled.ipynb
+.idea/Muscle_wasting.iml
+.ipynb_checkpoints/Untitled-checkpoint.ipynb
+*.tsv
+*.txt
+database_analysis/sql_operations.py
+*.jpg
+*.png

README.md

@@ -0,0 +1,104 @@
+<h1>Muscle_wasting</h1>
+
+<p>A bioinformatics pipeline for transcriptomic analysis of muscle wasting conditions. Integrates differential expression, transcription factor analysis, pathway enrichment, and network generation in a unified workflow.</p>
+
+<h2>🚀 Features</h2>
+<ul>
+  <li><strong>run_DEA</strong> – Perform Differential Expression Analysis (DEA) and extract Differentially Dysregulated Sites (DDSs).</li>
+  <li><strong>run_DDs</strong> – Identify Differentially Expressed Genes (DEGs).</li>
+  <li><strong>run_TF</strong> – Predict and analyze transcription factors driving the DEGs.</li>
+  <li><strong>run_pathway</strong> – Conduct pathway enrichment on DEGs or TF targets.</li>
+  <li><strong>run_network_creation</strong> – Build regulatory networks based on TF–gene relationships.</li>
+  <li><strong>main_pipeline</strong> – Execute the full workflow in sequence.</li>
+</ul>
+
+<h2>📁 Repository Structure</h2>
+<pre><code>Muscle_wasting/
+├── common_tools/          # Shared scripts and utilities
+├── database_analysis/     # Database-driven analyses
+├── data/                  # Raw/processed input data
+├── network/               # Network construction modules
+├── paper_mining/          # PubMed paper mining scripts
+├── cytoscape/             # Cytoscape-specific tools
+├── Databases/             # External data resources
+├── ncbi/                  # NCBI query modules
+├── Tests/                 # Unit and integration tests
+├── Constants.py           # Global constants and config
+├── main.py                # CLI entrypoint; defines main_pipeline
+├── requirements.txt       # Python dependencies
+└── DE_genes.ods           # Example DEG output file
+</code></pre>
+
+<h2>🛠️ Installation</h2>
+<p>Install required packages:</p>
+<pre><code>pip install -r requirements.txt</code></pre>
+
+<p>Main dependencies:</p>
+<ul>
+  <li>pandas</li>
+  <li>numpy</li>
+  <li>scipy</li>
+  <li>statsmodels (or DESeq2/edgeR via rpy2)</li>
+  <li>networkx</li>
+  <li>gseapy or enrichr</li>
+  <li>py4cytoscape</li>
+  <li>pytest</li>
+</ul>
+
+<h2>⚙️ Usage</h2>
+
+<h3>As a library:</h3>
+<pre><code>from main import run_DEA, run_DDs, run_TF, run_pathway, run_network_creation
+
+dds = run_DEA(input_counts, sample_metadata)
+degs = run_DDs(dds)
+tfs = run_TF(degs)
+pathways = run_pathway(degs)
+network = run_network_creation(tfs, degs)
+</code></pre>
+
+<h3>Via the command-line:</h3>
+<pre><code>python main.py \
+  --input counts.csv \
+  --metadata meta.csv \
+  --output_dir results/
+</code></pre>
+
+<p>This runs the full <code>main_pipeline</code>, sequentially performing:</p>
+<ol>
+  <li>DEA & DDS detection</li>
+  <li>DEG calling</li>
+  <li>TF analysis</li>
+  <li>Pathway enrichment</li>
+  <li>Network construction</li>
+</ol>
+
+<p>Results are stored in <code>results/</code> as CSV and graph files.</p>
+
+<h2>🧪 Testing</h2>
+<p>Run tests from the repo root:</p>
+<pre><code>pytest</code></pre>
+
+<h2>📄 Output</h2>
+<ul>
+  <li>DDS list</li>
+  <li>DEG list</li>
+  <li>Predicted TFs and regulators</li>
+  <li>Enriched pathway reports</li>
+  <li>Network export formats (e.g. SIF, GraphML)</li>
+</ul>
+
+<h2>📚 Citation</h2>
+<p>If you publish results using this pipeline, please cite the original <a href="https://github.com/GuerreroVazquez/Muscle_wasting">GuerreroVazquez/Muscle_wasting</a> repository.</p>
+
+<h2>❓ Questions & Contributing</h2>
+<p>For bugs, feature requests, or contributions, please open an issue or pull request.</p>
+
+<hr />
+
+<h3>Author</h3>
+<p>
+  Karen Guerrero‑Vazquez<br />
+  📧 <a href="mailto:Karen.GuerreroVazquez@gmail.com">GuerreroVazquez.Karen@gmail.com</a><br />
+  GitHub: <a href="https://github.com/GuerreroVazquez">GuerreroVazquez</a>
+</p>

Untitled.ipynb

@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

cytoscape/Data/Apps_details.json

@@ -0,0 +1,121 @@
+{
+  "gene_mania": {
+    "source": "gene_mania",
+    "node_keys": [
+      "id",
+      "shared_name",
+      "score",
+      "node_type",
+      "query_term",
+      "log_score",
+      "name",
+      "annotations",
+      "annotation_name",
+      "gene_name",
+      "SUID",
+      "selected"
+    ],
+    "edge_keys": [
+      "id",
+      "source",
+      "target",
+      "shared_name",
+      "highlight",
+      "normalized_max_weight",
+      "shared_interaction",
+      "raw_weights",
+      "name",
+      "interaction",
+      "SUID",
+      "networks",
+      "selected",
+      "data_type"
+    ],
+    "main_name": "gene_name"
+  },
+  "tf": {
+    "source": "tf",
+    "node_keys": [
+      "shared_name",
+      "name"
+    ],
+    "edge_keys": [
+      "shared_name",
+      "shared_interaction",
+      "name",
+      "interaction",
+      "weight",
+      "direction"
+    ],
+    "main_name": "name"
+  },
+  "stringdb": {
+    "edge_keys": [
+      "id",
+      "source",
+      "target",
+      "shared_name",
+      "stringdb_textmining",
+      "shared_interaction",
+      "stringdb_score",
+      "name",
+      "interaction",
+      "SUID",
+      "stringdb_coexpression",
+      "selected"
+    ],
+    "main_name": "name",
+    "node_keys": [
+      "id",
+      "compartment_golgi_apparatus",
+      "stringdb_namespace",
+      "tissue_urine",
+      "compartment_nucleus",
+      "stringdb_structures",
+      "tissue_saliva",
+      "stringdb_species",
+      "tissue_liver",
+      "compartment_extracellular",
+      "tissue_stomach",
+      "selected",
+      "compartment_endosome",
+      "tissue_heart",
+      "compartment_lysosome",
+      "stringdb_enhancedLabel_Passthrough",
+      "stringdb_canonical_name",
+      "tissue_eye",
+      "compartment_cytoskeleton",
+      "tissue_nervous_system",
+      "tissue_pancreas",
+      "target_family",
+      "tissue_bone",
+      "stringdb_node_type",
+      "name",
+      "tissue_muscle",
+      "stringdb_STRING_style",
+      "compartment_mitochondrion",
+      "target_development_level",
+      "tissue_lung",
+      "compartment_cytosol",
+      "tissue_skin",
+      "compartment_plasma_membrane",
+      "shared_name",
+      "stringdb_interactor_score",
+      "tissue_kidney",
+      "SUID",
+      "_id",
+      "compartment_endoplasmic_reticulum",
+      "stringdb_description",
+      "tissue_thyroid_gland",
+      "display_name",
+      "tissue_adrenal_gland",
+      "tissue_gall_bladder",
+      "stringdb_sequence",
+      "tissue_intestine",
+      "stringdb_database_identifier",
+      "tissue_blood",
+      "tissue_spleen"
+    ],
+    "source": "stringdb"
+  }
+}

cytoscape/Data/Apps_details.yaml

@@ -0,0 +1,108 @@
+stringdb:
+  edge_keys:
+  - id
+  - source
+  - target
+  - shared_name
+  - stringdb_textmining
+  - shared_interaction
+  - stringdb_score
+  - name
+  - interaction
+  - SUID
+  - stringdb_coexpression
+  - selected
+  main_name: name
+  node_keys:
+  - id
+  - compartment_golgi_apparatus
+  - stringdb_namespace
+  - tissue_urine
+  - compartment_nucleus
+  - stringdb_structures
+  - tissue_saliva
+  - stringdb_species
+  - tissue_liver
+  - compartment_extracellular
+  - tissue_stomach
+  - selected
+  - compartment_endosome
+  - tissue_heart
+  - compartment_lysosome
+  - stringdb_enhancedLabel_Passthrough
+  - stringdb_canonical_name
+  - tissue_eye
+  - compartment_cytoskeleton
+  - tissue_nervous_system
+  - tissue_pancreas
+  - target_family
+  - tissue_bone
+  - stringdb_node_type
+  - name
+  - tissue_muscle
+  - stringdb_STRING_style
+  - compartment_mitochondrion
+  - target_development_level
+  - tissue_lung
+  - compartment_cytosol
+  - tissue_skin
+  - compartment_plasma_membrane
+  - shared_name
+  - stringdb_interactor_score
+  - tissue_kidney
+  - SUID
+  - _id
+  - compartment_endoplasmic_reticulum
+  - stringdb_description
+  - tissue_thyroid_gland
+  - display_name
+  - tissue_adrenal_gland
+  - tissue_gall_bladder
+  - stringdb_sequence
+  - tissue_intestine
+  - stringdb_database_identifier
+  - tissue_blood
+  - tissue_spleen
+
+gene_mania:
+  edge_keys:
+  - id
+  - source
+  - target
+  - shared_name
+  - highlight
+  - normalized_max_weight
+  - shared_interaction
+  - raw_weights
+  - name
+  - interaction
+  - SUID
+  - networks
+  - selected
+  - data_type
+  main_name: gene_name
+  node_keys:
+  - id
+  - shared_name
+  - score
+  - node_type
+  - query_term
+  - log_score
+  - name
+  - annotations
+  - annotation_name
+  - gene_name
+  - SUID
+  - selected
+
+tf:
+  edge_keys:
+  - shared_name
+  - name
+  - interaction
+  - weight
+  - direction
+  main_name: name
+  node_keys:
+  - shared_name
+  - name

cytoscape/Data/properties_2_keep.yaml

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+all:
+  - id
+  - source
+  - target
+gene_mania:
+  - annotation_name
+  - score
+  - gene_name
+stringdb:
+  - tissue_urine
+tf:
+  - shared_name
+  - name