数据与复现蛋白结构与设计FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-isoform-switching

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

Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions. Use when investigating how splicing changes affect protein function.

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

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-isoform-switching

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

Identify isoform switches 、 predict their functional consequences on protein structure 、 function。
salmonQuant <- importIsoformExpression( parentDir = 'salmon_quant/'，addIsofomIdAsColumn = TRUE )。

原始文档

SKILL.md 摘录

IsoformSwitchAnalyzeR Workflow

Goal: Identify genes where the dominant isoform switches between conditions.

Approach: Import Salmon quantification, filter low-expression isoforms, and test for isoform usage changes with DEXSeq-based statistics.

"Analyze isoform switching" -> Import transcript quantification, test for dominant isoform changes, and assess functional consequences.

R: IsoformSwitchAnalyzeR (importRdata + isoformSwitchTestDEXSeq)

library(IsoformSwitchAnalyzeR)

## Create switch analysis object

switchAnalyzeRlist <- importRdata(
    isoformCountMatrix = salmonQuant$counts,
    isoformRepExpression = salmonQuant$abundance,
    designMatrix = data.frame(
        sampleID = colnames(salmonQuant$counts),
        condition = c('control', 'control', 'control', 'treatment', 'treatment', 'treatment')
    ),
    isoformExonAnnoation = 'annotation.gtf',
    isoformNtFasta = 'transcripts.fa'
)

## Filter lowly expressed isoforms

switchAnalyzeRlist <- preFilter(
    switchAnalyzeRlist,
    geneExpressionCutoff = 1,  # Minimum TPM
    isoformExpressionCutoff = 0,
    removeSingleIsoformGenes = TRUE
)