IOBRpy Book

Authors

Haonan Huang

Dongqiang Zeng

IOBRpy is a command-line toolkit for bulk RNA-seq tumor microenvironment (TME) analysis. It wires together FASTQ QC, quantification (Salmon or STAR), matrix assembly, signature scoring, immune deconvolution, clustering, and ligand–receptor scoring.

0.1 Input Requirements

FASTQ layout: paired-end by default. Filenames end with *_1.fastq.gz / *_2.fastq.gz (configurable via --suffix1).
Expression matrix orientation: genes × samples by default.
Output file delimiters: automatically inferred from the file extension; .csv and .tsv/.txt are recommended.