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splicing-quantification

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

When to use

• measuring splice-site usage
• measuring isoform inclusion ratios
• quantifying alternative splicing events as PSI
• analyzing short-read RNA-seq data
• detecting canonical event classes (SE, A5SS, A3SS, MXE, RI)
• detecting special classes (microexons, exitrons, AFE/ALE)
• analyzing intron retention subtypes
• applying effective-length normalization

When not to use

• tasks not involving short-read RNA-seq
• tasks not measuring splice-site usage or isoform inclusion ratios

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