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

bio-splicing-quantification

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

Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative splice sites, mutually exclusive exons, and retained introns. Use when measuring splice site usage or isoform ratios from RNA-seq data.

OpenClawNanoClaw分析处理复现实验bio-splicing-quantification🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcquantifies

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Quantify alternative splicing events as PSI (percent spliced in) values ，面向 RNA-seq data。
subprocess.run([ 'suppa.py'，'generateEvents'，'-i'，gtf_file，'-o'，output_prefix，'-f'，'ioe'，# IOE format ，用于 PSI calculation '-e'，'SE'，'SS'，'MX'，'RI'，'FL' # All event types ]，check=True)。

原始文档

SKILL.md 摘录

Event Types

Type	Code	Description
Skipped exon	SE	Exon inclusion/exclusion
Alternative 5' splice site	A5SS	Alternative donor site
Alternative 3' splice site	A3SS	Alternative acceptor site
Mutually exclusive exons	MXE	One of two exons included
Retained intron	RI	Intron retention

SUPPA2 (transcript TPM-based)

Input: Transcript TPM from Salmon/kallisto
Faster, requires transcript quantification
Better for isoform-level analysis

rMATS-turbo (BAM-based)

Input: Aligned BAM files
Junction read counting
Better for novel junction discovery

适用场景

适合在measuring splice site usage 或 isoform ratios ，面向 RNA-seq data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

differential-splicing - Compare PSI between conditions
rna-quantification/alignment-free-quant - Generate transcript TPM for SUPPA2
read-alignment/star-alignment - Align reads with junction detection

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