Installation

Requirements

Requirement	Version
Python	3.9, 3.10, or 3.11
pip	latest recommended
MAGMA (optional)	for GWAS enrichment (rgs step)

Note: Python 3.12+ is currently not supported due to upstream dependency constraints.

---

Install via PyPI (Recommended)

pip install scRBP

Verify installation:

scRBP --help

---

Install from Source

git clone https://github.com/mayunlong89/scRBP.git
cd scRBP
pip install -e .

---

Install in a Conda Environment (Recommended)

# Create a dedicated environment
conda create -n scrbp python=3.10
conda activate scrbp

# Install scRBP
pip install scRBP

---

Install on HPC / Cluster

# Load modules (example for SLURM clusters)
module load anaconda3

# Create isolated environment
conda create -n scrbp python=3.10 -y
conda activate scrbp

# Install with all dependencies
pip install scRBP

# Verify
scRBP --help

For large datasets (>300,000 cells), we recommend running getSketch first to downsample to ~50,000 cells before GRN inference.

---

Optional: MAGMA for GWAS Enrichment

The rgs step requires the MAGMA binary for gene-set GWAS enrichment analysis.

1. Download MAGMA from the official website
2. Add MAGMA to your system PATH:

export PATH="/path/to/magma:$PATH"

1. Verify:

magma --version

---

Key Dependencies

Package	Purpose
numpy, pandas, scipy	Numerical computation
anndata, scanpy	Single-cell data I/O
arboreto	GRNBoost2 / GENIE3 inference
pyscenic, ctxcore	Motif enrichment pruning
geosketch	Stratified cell downsampling
polars, pyarrow	High-performance data processing

---

Supported File Formats

Format	Extension	Used For
AnnData	.h5ad	Expression matrix (recommended)
Feather	.feather	Fast tabular exchange
Loom	.loom	Single-cell data
CSV	.csv	Expression or output scores
GMT	.gmt	Regulon gene sets
TSV	.tsv	Network edge lists