Statistical Genetics Single-cell genomics RBP regulatory networks

All scRBP commands follow the pattern:

scRBP <command> [options]

Run scRBP --help or scRBP <command> --help for full option listings.

Commands Overview

Command Description
getSketch Stratified cell downsampling via GeoSketch (Optional)
getGRN GRN inference using GRNBoost2 or GENIE3 (--mode gene/isoform)
getMerge_GRN Consensus network merging across N seeds
getModule Regulon candidate extraction (Top-N / Percentile strategies)
getPrune Motif enrichment filtering via ctxcore (NES scoring)
getRegulon GMT file generation (gene symbol + Entrez ID)
mergeRegulons Merge 4 region-specific GMT files (3UTR/5UTR/CDS/Introns)
ras Regulon Activity Score via AUCell (--mode sc/ct)
rgs Regulon-level Genetic association Score via MAGMA (--mode sc/ct)
trs Trait Relevance Score by integrating RAS and RGS (--mode sc/ct)

getSketch

scRBP getSketch --input INPUT --output OUTPUT [options]
Option Type Default Description
--input path required Input .h5ad or .feather file
--output path required Output file (.h5ad / .feather / .csv / .npz)
--n_cells int 250000 Target total number of cells to sketch
--n_pca int 100 Number of PCA components for GeoSketch
--celltype_col str celltype Cell-type column in adata.obs (.h5ad input only)
--min_cells_per_type int 50 Minimum cells per cell type (.h5ad input only)
--seed int 42 Random seed

getGRN

scRBP getGRN --matrix MATRIX --rbp_list RBP_LIST --output OUTPUT [options]
Option Type Default Description
--matrix path required Expression matrix (.csv / .csv.gz / .feather / .loom)
--rbp_list path required RBP list file (gene symbols, one per line)
--output path required Output GRN .tsv file
--method str grnboost2 Algorithm: grnboost2 or genie3
--mode str gene Inference mode: gene (RBP→gene) or isoform (RBP→isoform)
--isoform_annotation path None Isoform→gene annotation (required for --mode isoform)
--n_workers int all CPUs Number of parallel workers
--batch_size int 10 Number of outer batches
--threshold float 0.03 Absolute Spearman correlation threshold
--correlation bool True Compute Spearman correlation and Mode columns
--seed int 1234 Random seed

getMerge_GRN

scRBP getMerge_GRN --pattern "GLOB" --output OUTPUT [options]
Option Type Default Description
--pattern str required Glob pattern matching all seed GRN .tsv files
--output path required Output merged GRN .tsv
--corr-threshold float 0.0 Filter edges with abs(mean Correlation) ≤ threshold
--n_present int 0 Min number of seed runs an edge must appear in
--present_rate float 0.0 Min presence rate (n_present / N_runs) to keep an edge

getModule

scRBP getModule --input INPUT --output_merged OUTPUT [options]
Option Type Default Description
--input path required Merged GRN .tsv from getMerge_GRN
--output_merged path required Output merged modules .tsv
--importance_threshold float 0.005 Minimum importance score to retain an edge
--top_n_list str "5,10,50" Comma-separated Top-N values for selection
--target_top_n str "50" Target Top-N for merged output
--percentile str "0.75,0.9" Comma-separated percentile thresholds
--verbose flag False Enable verbose logging

getPrune

scRBP getPrune --rbp_targets RBP_TARGETS --motif_rbp_links MOTIF_RBP_LINKS \
               --motif_target_ranks RANKINGS --save_dir SAVE_DIR [options]
Option Type Default Description
--rbp_targets path required Module .tsv from getModule
--motif_rbp_links path required Motif–RBP annotation .feather
--motif_target_ranks path required Genome rankings .feather (e.g. hg38_500bp_rankings.feather)
--save_dir path required Output directory for pruned scores (Parquet)
--rank_threshold int 1500 Top-N rank cutoff for motif enrichment
--auc_threshold float 0.05 AUC threshold for enrichment significance
--nes_threshold float 3.0 Normalized Enrichment Score threshold
--min_genes int 20 Minimum target genes to retain a regulon
--n_jobs int all CPUs Number of parallel processes
--chunksize int 4 Multiprocessing chunk size
--only_rbp str None Restrict to a specific RBP (debugging)
--only_strategy str None Restrict to a specific selection strategy

getRegulon

scRBP getRegulon --input INPUT --out-symbol OUT_SYMBOL --out-entrez OUT_ENTREZ [options]
Option Type Default Description
--input path required Pruned ctxcore .csv from getPrune
--out-symbol path required Output GMT file (gene symbols)
--out-entrez path required Output GMT file (Entrez IDs)
--rbp_col str RBP Column name for RBP in input CSV
--genes_col str auto Column name for target genes (auto-detected)
--min_genes int 1 Minimum targets to retain a regulon
--taxid int 9606 NCBI Taxonomy ID (9606=human, 10090=mouse)
--map-hgnc path None HGNC table for symbol→Entrez mapping
--map-ncbi path None NCBI gene info file for symbol→Entrez mapping
--drop-unmapped-genes flag False Drop genes that cannot be mapped to Entrez IDs
--drop-empty-sets flag False Drop regulons with zero genes after mapping

mergeRegulons

scRBP mergeRegulons --base_dir BASE_DIR --input GMT_FILENAME --output GMT_FILENAME [options]
Option Type Default Description
--base_dir path required Base directory containing region subdirectories
--input str required Input GMT filename to find in each region directory
--output str required Output merged GMT filename
--region_order list 3UTR 5UTR CDS Introns Order in which regions are merged
--region_glob str Results_final_*_RBP_top1500_* Glob for region-specific subdirectories
--tissue_glob str z_GRNBoost2_*_30times Glob for parent tissue dirs (with --recursive)
--recursive flag False Recursively process multiple parent directories
--dedup_lines flag False Deduplicate identical GMT lines
--overwrite flag False Overwrite existing output files
--summary_out path None Optional output .tsv for region-level summary

ras

scRBP ras --mode MODE --matrix MATRIX --regulons REGULONS --out OUT [options]
Option Type Default Description
--mode str ct Scoring mode: sc (per cell) or ct (per cell type)
--matrix path required Expression matrix (.h5ad / .feather / .loom / .csv)
--regulons path required Regulon GMT file from mergeRegulons
--out path required Output RAS file
--out_format str csv Output format: csv, loom, or both
--celltypes-csv path None CSV with cell_id, cell_type columns (required for --mode ct)
--cell-col str auto Cell ID column in --celltypes-csv
--ctype-col str auto Cell-type column in --celltypes-csv
--n_workers int 4 Workers for AUCell computation
--min_genes int 1 Drop regulons with fewer than N targets
--to_upper flag False Uppercase gene symbols when matching regulons

rgs

scRBP rgs --mode MODE --magma MAGMA --genes-raw GENES_RAW \
          --sets SETS --out OUT [options]
Option Type Default Description
--mode str required sc (single-cell) or ct (cell-type)
--magma path required Path to MAGMA binary
--genes-raw path required MAGMA <prefix>.genes.raw from prior gene analysis
--sets path required Regulon GMT file (Entrez or symbol format)
--id-type str entrez Gene ID format in GMT: entrez or symbol
--out str required Output file prefix
--n-null int 1000 Number of matched null regulons
--seed int 2025 Random seed for null sampling
--q-bins int 10 Quantile bins for null matching
--threads int auto CPU threads for MAGMA
--gene-loc path None MAGMA NCBI*.gene.loc for Entrez↔Symbol mapping
--min_genes int 0 Minimum regulon size
--cleanup-out bool True Remove intermediate MAGMA output files
--expr-stats path None Precomputed expression stats TSV

trs

scRBP trs --mode MODE --ras RAS --rgs-csv RGS_CSV --out-prefix PREFIX [options]
Option Type Default Description
--mode str required sc (single-cell) or ct (cell-type)
--ras path required RAS .csv from ras step
--rgs-csv path required RGS .csv from rgs step
--out-prefix str required Output file prefix
--rgs-score str mlog10p RGS score to use: mlog10p or z
--lambda-penalty float 1.0 Penalty for RAS–RGS divergence (λ)
--q-hi-ras float 0.99 Upper quantile cap for RAS normalization
--q-hi-rgs float 0.99 Upper quantile cap for RGS normalization
--do-fdr int 1 Apply BH-FDR correction (1=yes, 0=no; CT mode only)
--celltypes-csv path None CSV with cell_id, cell_type columns (CT mode)
--min_cells_pert_ct int 25 Minimum cells per cell type (CT mode)