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splicekit: splicing analysis from short-read RNA-seq

splicekit

splicekit is a modular, integrative platform for splicing analysis of short-read RNA-seq data. Starting from aligned reads (BAM files) and a sample annotation table, it defines test-vs-control comparisons, builds per-feature count tables (junctions, anchors, exons, genes), and runs a battery of splicing analyses — differential feature usage with edgeR, motif and RNA-protein binding enrichment, junction-vs-gene expression comparisons and more — all self-contained in a single project folder. It integrates pybio for genome operations, scanRBP for RNA-protein binding, and ships its own JBrowse2 instance for browsing results.

# create and activate the conda/micromamba environment, install splicekit
micromamba create -y -f splicekit.yaml
micromamba activate splicekit
./install.sh
pip install .

# run the full pipeline with Snakemake
./run_snakemake_local.sh --configfile config.yaml

What's included

  • Comparisons from a sample sheet — define test/control comparisons straight from samples.tab, optionally grouped or separated by extra columns. See Sample annotation.
  • Feature count tables — junctions, anchors, exons and genes, built from BAM files. See Features & count tables.
  • Differential splicing with edgeR — per-feature differential usage results, linked directly to JBrowse2. See Differential splicing (edgeR).
  • Motif & RNA-protein binding analysis — donor/acceptor motif logos, DREME enrichment and scanRBP binding analysis. See Motif & RNA-binding analysis.
  • juDGE plots — junction logFC vs. gene logFC, distinguishing splicing modifiers from expression modifiers. See juDGE plots.
  • Promiscuity, clustering, JUNE and rMATS analyses — see Additional analyses.
  • Integrated JBrowse2 + HTML report — one local web server for both. See Exploring results.

Where to start

New to splicekit? Read Installation and then Quick Start — together they take you from a fresh checkout to a running pipeline on example data in a few commands. Everything else in these docs is reference material for the individual analysis steps, configuration parameters and file formats.