IOBRpy

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.

Documentation

A complete documentation for IOBRpy can be found at https://iobr.github.io/IOBRpy/.

Agent Bootstrap

If you want coding agents to discover iobrpy-cli and the result-visualization skill without repeating them in every prompt, install the packaged agent integrations once:

# Claude Code: install `/iobrpy`, `/iobrpy-result`, and MCP registration
iobrpy-cli agent install --client claude-code

# Codex: install both skills, both plugins, and MCP registration
iobrpy-cli agent install --client codex

# Configure every supported client in one pass
iobrpy-cli agent install --client all

# Inspect what is already installed without changing anything
iobrpy-cli agent status

After installing the Claude Code/Codex integration, restart Claude Code/Codex once so the slash-command list refreshes.

Agent Entry Points

IOBRpy provides two agent entrypoints:

• /iobrpy helps you inspect input data, choose the right IOBRpy workflow, and prepare or run commands.
• /iobrpy-result is for finished outputs. It helps summarize, audit, interpret, compare, and visualize IOBRpy result directories or result tables.

In short, use /iobrpy before or during analysis, and use /iobrpy-result after results have been generated.

Examples:

/iobrpy please scan path/to/your/target/directory
/iobrpy-result visualize and interpret path/to/iobrpy/result/directory

Installation

Quick install

# Method 1 : PyPI
pip install iobrpy

# Method 2 : Conda (bioconda via conda-forge + bioconda)
conda install -c conda-forge -c bioconda iobrpy

# Method 3 : Docker
docker pull hhn123123/iobrpy:latest

PyPI

# Creating a virtual environment is recommended
conda create -n iobrpy python=3.11 -y
conda activate iobrpy

# Update pip
python -m pip install --upgrade pip

# Install iobrpy
pip install iobrpy

# Install fastp, salmon, STAR and MultiQC
# Recommended: use mamba for faster solves (if available)
mamba install -y -c conda-forge -c bioconda \
  fastp \
  salmon \
  star \
  trust4 \
  samtools=1.21

# If you don't have mamba, use conda instead
conda install -y -c conda-forge -c bioconda \
  fastp \
  salmon \
  star \
  trust4 \
  samtools=1.21

Conda

Prerequisite (Conda): Please install Miniconda or Anaconda first. We recommend Miniconda.

# Creating a virtual environment is recommended
conda create -n iobrpy python=3.11 -y
conda activate iobrpy

# Install iobrpy from bioconda via conda-forge + bioconda
# Recommended: use mamba for faster solves (if available)
mamba install -y -c conda-forge -c bioconda iobrpy

# If you don't have mamba, use conda instead
conda install -y -c conda-forge -c bioconda iobrpy

Features

End-to-End Pipeline Runner

• runall — A single command that wires the full Salmon or STAR pipeline end-to-end and writes the standardized layout: The pipeline creates the following directories, in order: 01-qc/, 02-salmon/ or 02-star/, 03-tpm/, 04-signatures/, 05-tme/, and 06-LR_cal/.

All-in-one TME profiling

• tme_profile - A single command that inputs a TPM (genes×samples) matrix, performs signature scoring, runs six immune deconvolution methods, merges their outputs, and computes ligand–receptor scores, using the functions calculate_sig_score, cibersort, IPS, estimate, mcpcounter, quantiseq, epic, and LR_cal.

Preprocessing

• fastq_qc — Parallel FASTQ QC/trimming via fastp, with per-sample HTML/JSON and an optional MultiQC summary report under 01-qc/multiqc_report/. Resume-friendly and prints output paths first.

Salmon submodule (quantification, merge, and TPM)

• batch_salmon — Batch salmon quant on paired-end FASTQs; safe R1/R2 inference; per-sample quant.sf; progress and preflight checks (salmon version, index meta).
• merge_salmon — Recursively collect per-sample quant.sf and produce two matrices: TPM and NumReads.
• prepare_salmon — Clean up Salmon outputs into a TPM matrix; strip version suffixes; keep symbol/ENSG/ENST identifiers.

STAR submodule (alignment, counts, and TPM)

• batch_star_count — Batch STAR alignment with --quantMode GeneCounts, sorted BAM + _ReadsPerGene.out.tab; resume-friendly summary.
• merge_star_count — Merge multiple _ReadsPerGene.out.tab into one wide count matrix.
• count2tpm — Convert counts to TPM (supports Ensembl/Entrez/Symbol/MGI; optional effective length CSV).

Expression Annotation & Mouse to Human Mapping & log2(x+1) (Optional)

• anno_eset — Harmonize/annotate an expression matrix (choose symbol/probe columns; deduplicate; aggregation method).
• mouse2human_eset — Convert mouse gene symbols to human gene symbols. Supports two modes: matrix mode (rows = genes) or table mode (input contains a symbol column).
• log2_eset — Apply log2(x+1) to a genes × samples expression matrix.

Pathway / signature scoring

• calculate_sig_score — Sample‑level signature scores via pca, zscore, ssgsea, or integration. Supports the following signature groups (space‑ or comma‑separated), or all to merge them:
  • go_bp, go_cc, go_mf
  • signature_collection, signature_tme, signature_sc, signature_tumor, signature_metabolism
  • kegg, hallmark, reactome

Immune deconvolution and scoring

• cibersort — CIBERSORT wrapper/implementation with permutations, quantile normalization, absolute mode.
• quantiseq — quanTIseq deconvolution with lsei or robust norms (hampel, huber, bisquare); tumor‑gene filtering; mRNA scaling.
• epic — EPIC cell fractions using TRef/BRef references.
• estimate — ESTIMATE immune/stromal/tumor purity scores.
• mcpcounter — MCPcounter infiltration scores.
• IPS — Immunophenoscore (AZ/SC/CP/EC + total).
• bayesprism — Bayesian deconvolution with a single-cell reference; standalone optional workflow outside the default tme_profile / runall six-method bundle.

Clustering / decomposition

• tme_cluster — k‑means with automatic k via KL index (Hartigan–Wong), feature selection and standardization.
• nmf — NMF‑based clustering (auto‑selects k; excludes k=2) with PCA plot and top features.

Ligand–receptor

• LR_cal — Ligand–receptor interaction scoring using cancer‑type specific networks.

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.

Command‑line usage

From FASTQ to TME - runall

How runall passes options

runall defines a small set of top-level options (e.g., --mode/--outdir/--fastq/--threads/--batch_size). Any unrecognized options are forwarded to the corresponding sub-steps. This keeps runall flexible as sub-commands evolve.

Below are two fully wired workflows handled by iobrpy runall.

Salmon mode

iobrpy runall \
  --mode salmon \
  --outdir "/path/to/outdir" \
  --fastq "/path/to/fastq" \
  --threads 8 \
  --batch_size 1 \
  --index "/path/to/salmon/index" \
  --project MyProj

STAR mode

iobrpy runall \
  --mode star \
  --outdir "/path/to/outdir" \
  --fastq "/path/to/fastq" \
  --threads 8 \
  --batch_size 1 \
  --index "/path/to/star/index" \
  --project MyProj

Option legend for the runall examples

Common options

Expected layout

# Salmon mode：
/path/to/outdir
|-- 01-qc
|   |-- <sample>_1.fastq.gz
|   |-- <sample>_2.fastq.gz
|   |-- <sample>_fastp.html
|   |-- <sample>_fastp.json
|   |-- <sample>.task.complete
|   `-- multiqc_report
|       `-- multiqc_fastp_report.html
|-- 02-salmon
|   |-- <sample>
|   |   `-- quant.sf
|   |-- MyProj_salmon_count.tsv.gz
|   `-- MyProj_salmon_tpm.tsv.gz
|-- 03-tpm
|   |-- prepare_salmon.csv
|   `-- tpm_matrix.csv
|-- 04-signatures
|   `-- calculate_sig_score.csv
|-- 05-tme
|   |-- cibersort_results.csv
|   |-- epic_results.csv
|   |-- quantiseq_results.csv
|   |-- IPS_results.csv
|   |-- estimate_results.csv
|   |-- mcpcounter_results.csv
|   `-- deconvo_merged.csv
`-- 06-LR_cal
    `-- lr_cal.csv
# STAR mode：
/path/to/outdir
|-- 01-qc
|   |-- <sample>_1.fastq.gz
|   |-- <sample>_2.fastq.gz
|   |-- <sample>_fastp.html
|   |-- <sample>_fastp.json
|   |-- <sample>.task.complete
|   `-- multiqc_report
|       `-- multiqc_fastp_report.html
|-- 02-star
|   |-- <sample>/
|   |-- <sample>__STARgenome/
|   |-- <sample>__STARpass1/
|   |-- <sample>_STARtmp/
|   |-- <sample>_Aligned.sortedByCoord.out.bam
|   |-- <sample>_Log.final.out
|   |-- <sample>_Log.out
|   |-- <sample>_Log.progress.out
|   |-- <sample>_ReadsPerGene.out.tab
|   |-- <sample>_SJ.out.tab
|   |-- <sample>.task.complete
|   |-- .batch_star_count.done
|   |-- .merge_star_count.done
|   `-- MyProj.STAR.count.tsv.gz
|-- 03-tpm
|   |-- count2tpm.csv
|   `-- tpm_matrix.csv
|-- 04-signatures
|   `-- calculate_sig_score.csv
|-- 05-tme
|   |-- cibersort_results.csv
|   |-- epic_results.csv
|   |-- quantiseq_results.csv
|   |-- IPS_results.csv
|   |-- estimate_results.csv
|   |-- mcpcounter_results.csv
|   `-- deconvo_merged.csv
`-- 06-LR_cal
    `-- lr_cal.csv

Output Reference

Standard layout (produced by iobrpy runall)

• 01-qc/ — fastp outputs; a resume flag .fastq_qc.done is written when the step completes.
• 02-salmon/ or 02-star/ — quantification/alignment + merged matrices; resume flags like .batch_salmon.done, .merge_salmon.done, or .merge_star_count.done.
• 03-tpm/ — unified TPM matrix tpm_matrix.csv. For Salmon mode it comes from prepare_salmon; for STAR mode it comes from count2tpm.
• 04-signatures/ — signature scoring results (file: calculate_sig_score.csv).
• 05-tme/ — deconvolution outputs from multiple methods + deconvo_merged.csv.
• 06-LR_cal/ — ligand–receptor results lr_cal.csv.

Salmon mode (02-salmon/)

• Per-sample Salmon folders containing quant.sf (from batch_salmon). A .batch_salmon.done flag is written after completion.
• Merged matrices (from merge_salmon):
  • <PROJECT>_salmon_tpm.tsv[.gz]
  • <PROJECT>_salmon_count.tsv[.gz]
    A .merge_salmon.done flag is written after completion.
• 03-tpm/prepare_salmon.csv — cleaned genes × samples TPM matrix produced by prepare_salmon (default --return_feature symbol unless overridden).
• 03-tpm/tpm_matrix.csv — log2(x+1) matrix produced by log2_eset from prepare_salmon.csv.

STAR mode (02-star/)

• Per-sample STAR outputs (BAM, logs, *_ReadsPerGene.out.tab, etc.).
• Merged counts (from merge_star_count):
  • <PROJECT>.STAR.count.tsv.gz . A .merge_star_count.done flag is written after completion.
• 03-tpm/count2tpm.csv — TPM matrix produced by count2tpm from the merged STAR ReadPerGene/count matrix.
• 03-tpm/tpm_matrix.csv — log2(x+1) matrix produced by log2_eset from count2tpm.csv.

Signatures (04-signatures/)

• calculate_sig_score.csv — per-sample pathway/signature scores. Columns correspond to the selected signature set and method (integration, pca, zscore, or ssgsea).

Deconvolution (05-tme/)

Each method writes a single table named <method>_results.csv:

• cibersort_results.csv — columns suffixed with _CIBERSORT. Note whether --perm and --QN were used.
• quantiseq_results.csv — quanTIseq fractions. Document the chosen --method {lsei|hampel|huber|bisquare} and flags like --arrays, --tumor, --scale_mrna, --signame.
• epic_results.csv — EPIC fractions; record the reference profile used (--reference {TRef|BRef|both}).
• estimate_results.csv — ESTIMATE immune/stromal/purity scores; columns suffixed _estimate.
• mcpcounter_results.csv — MCPcounter scores; columns suffixed _MCPcounter.
• IPS_results.csv — IPS sub-scores and total score.

Merged table

• deconvo_merged.csv — produced by runall after all deconvolution methods finish; normalizes the sample index to a column named ID and outer-joins by sample ID across methods.

Ligand–receptor (06-LR_cal/)

• lr_cal.csv — ligand–receptor scoring table from LR_cal. Record the --data_type {count|tpm} and the --id_type you used.

Contact / Support

• Issues: https://github.com/IOBR/IOBRpy/issues
• Maintainers: [ Haonan Huang ] (email = 2905611068@qq.com); [ Dongqiang Zeng ] (email = interlaken@smu.edu.cn)