Metadata-Version: 2.4
Name: GeneXpressor
Version: 0.1.4
Summary: DESeq2 runner (Python + rpy2) for bulk RNA-seq with auto-discovery, E2E DE, plots, HTML report.
Project-URL: Homepage, https://github.com/shari01/GeneXpressor
Author-email: Sheryar Malik <sheryarmalik1403@gmail.com>
License: MIT
Keywords: DESeq2,RNA-seq,bioinformatics,differential-expression,rpy2
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Requires-Dist: rpy2>=3.5
Description-Content-Type: text/markdown

# GeneXpressor

A friendly DESeq2 runner driven from Python via rpy2. It auto-discovers your counts/metadata, produces plots, CSVs, and an optional HTML report.

## Requirements
- **R** (≥ 4.x) installed and on PATH (on Windows set `R_HOME` or install R normally)
- R packages: `DESeq2`, `BiocParallel`, `dplyr`, `ggplot2`, `ggrepel`, `pheatmap`, `readr`, `tidyr`, `tibble`, `rmarkdown`, `RColorBrewer`
  - (optional) `readxl`, `arrow` for Excel/feather/parquet
- Python: `rpy2`

## Install (editable)
```bash
pip install -e .


arguments

genexpressor \                                                                                                                                 
>>   --parent_dir "C:\Users\shahr\Downloads\Deseq2-pkg" \
>>   --pick AUTO \
>>   --case_level Disease --control_level Control \
>>   --alpha 0.05 --lfc_thr 2.0 --top_labels 20 --top_heatmap 50 \
>>   --make_report true --debug true --threads 2