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bio-differential-splicing

Maintainer FreedomIntelligence · Last updated April 1, 2026

Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

OpenClawNanoClawAnalysisReproductionbio-differential-splicing🧬 bioinformatics (gptomics bio-* suite)bioinformatics — differential expression & transcriptomicsdetects

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-differential-splicing

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Detect differential alternative splicing events between experimental conditions.
  • rmats.py \ --b1 condition1_bams.txt \ --b2 condition2_bams.txt \ --gtf annotation.gtf \ -t paired \ --readLength 150 \ --nthread 8 \ --od rmats_output \ --tmp rmats_tmp python import pandas as pd.

Source Doc

Excerpt From SKILL.md

Tool Comparison

ToolInputApproachStrengths
rMATS-turboBAMJunction countingNovel junctions, statistical model
SUPPA2TPMTranscript ratiosSpeed, isoform-aware
leafcutterBAMIntron clusteringNovel events, no annotation bias

rMATS-turbo Analysis

Goal: Detect statistically significant differential splicing events between two conditions from BAM files.

Approach: Run rMATS-turbo on condition-grouped BAMs, then filter results by FDR and delta PSI thresholds.

"Find differential splicing between conditions" -> Compare junction-level inclusion across sample groups with statistical testing.

  • CLI/Python: rmats.py + pandas filtering (rMATS-turbo)
  • Python/CLI: suppa.py diffSplice (SUPPA2, TPM-based)
  • R: leafcutter_ds.R (leafcutter, annotation-free)

## Load results for skipped exons

se = pd.read_csv('rmats_output/SE.MATS.JC.txt', sep='\t')

Use cases

  • Use when comparing splicing patterns between treatment groups, tissues, or disease states.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • splicing-quantification - Calculate PSI values first
  • isoform-switching - Functional consequence analysis
  • sashimi-plots - Visualize significant events
  • read-alignment/star-alignment - STAR 2-pass alignment required

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