GeneXpressor 0.1.4

DESeq2 runner (Python + rpy2) for bulk RNA-seq with auto-discovery, E2E DE, plots, HTML report.

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)

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