数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-differential-splicing

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-differential-splicing🧬 bioinformatics (gptomics bio-* suite)bioinformatics — differential expression & transcriptomicsdetects

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

检测 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。

原始文档

SKILL.md 摘录

Tool Comparison

Tool	Input	Approach	Strengths
rMATS-turbo	BAM	Junction counting	Novel junctions, statistical model
SUPPA2	TPM	Transcript ratios	Speed, isoform-aware
leafcutter	BAM	Intron clustering	Novel 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')

适用场景

适合在comparing splicing patterns between treatment groups，tissues，或 disease states时使用。

不适用场景

Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

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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