add usage for external validation

Author: RibaA

docs/usage.md

@@ -1,5 +1,101 @@
 # Usage Guide
 
+This section provides step-by-step instructions to configure, run, and manage your analysis.
+
+---
+
 ## Project Configuration
 
-Farnoosh is working on that
+### 1. Customize Configuration Files
+
+Edit the YAML files in the `config/` directory to reflect your study parameters:
+- `config_rnaseq_io.yaml`: For processing raw input into analysis-ready format.
+
+Each center should create a center-specific config file using the template:
+
+```bash
+config/<center_or_study_name>.yaml
+# Example:
+config/ICB_Gide.yaml
+```
+
+Use `config/config_local.yaml` as a reference.
+
+---
+
+### 2. Add Input Data
+
+Place your raw input datasets (e.g., `.rds` files) in the `data/rawdata/` directory:
+
+```bash
+data/rawdata/ICB_Gide.rds
+```
+
+Also include gene signature metadata files:
+
+- `signature.rda`
+- `signature_information.csv`
+- Precompiled `.RData` file — [Zenodo DOI: 10.5281/zenodo.18509237](https://doi.org/10.5281/zenodo.18509237)
+
+---
+
+## Running Your Analysis
+
+### 1. Install Dependencies
+
+If using [`pixi`](https://prefix.dev/docs/pixi/overview):
+
+```bash
+pixi install
+```
+
+This sets up your environment with R, Bioconductor, and required packages.
+
+---
+
+### 2. Run Local Processing
+
+Prepare analysis-ready `.rda` files from raw data:
+
+```bash
+Rscript workflow/scripts/runProcData.R
+```
+
+---
+
+### 3. Run Signature Scoring 
+
+```bash
+Rscript workflow/scripts/runSigScore.R
+```
+
+---
+
+### 4. Run Association-analysis
+
+```bash
+Rscript workflow/scripts/runSigAssoc.R
+```
+
+### 5. Run Meta-analysis 
+
+```bash
+Rscript workflow/scripts/runMeta.R
+```
+
+---
+
+### 6. Generate Visualizations
+
+```bash
+Rscript workflow/scripts/runVisualization.R
+```
+
+This script generates forest plots, volcano plots, and heatmaps.
+**Note**: `runSigCluster.R` and `runCorr.r` are considered to study signatures' distributions. 
+
+---
+
+## Tips for Managing Your Data
+
+- Use meaningful filenames (e.g., `ICB_Gide__Melanoma__PD-(L)1.rda`)