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bio-chipseq-differential-binding
维护者 FreedomIntelligence · 最近更新 2026年4月1日
bio-chipseq-differential-binding：Differential binding analysis ，使用 DiffBind。 比较 ChIP-seq peaks between conditions ，支持 statistical rigor。 适合在comparing ChIP-seq binding between conditions时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-differential-binding
- 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
核心说明
- R：DiffBind：：dba() → dba.count() → dba.contrast() → dba.analyze()。
- 比较 ChIP-seq binding between conditions" → Identify genomic regions ，支持 statistically significant differences in transcription factor 或 histone mark occupancy between experimental groups. R：DiffBind：：dba() → dba.count() → dba.contrast() → dba.analyze()。
- samples <- data.frame( SampleID = c('ctrl_1'，'ctrl_2'，'treat_1'，'treat_2')，Tissue = c('cell'，'cell'，'cell'，'cell')，Factor = c('H3K4me3'，'H3K4me3'，'H3K4me3'，'H3K4me3')，Condition = c('control'，'control'，'treatment'，'treatment')，Replicate = c(1，2，1，2)，bamReads = c('ctrl1.bam'，'ctrl2.bam'，'treat1.bam'，'treat2.bam')，Peaks = c('ctrl1_peaks.narrowPeak'，'ctrl2_peaks.narrowPeak'，'treat1_peaks.narrowPeak'，'treat2_peaks.narrowPeak')，PeakCaller = c('macs'，'macs'，'macs'，'macs') )。
- 撰写.csv(samples，'samples.csv'，row.names = FALSE)。
原始文档
SKILL.md 摘录
Create Sample Sheet
Goal: Define the experimental design linking BAM files, peak files, and sample metadata for DiffBind.
Approach: Build a data frame (or CSV) with required columns mapping each sample to its files and conditions.
## Load Data
**Goal:** Initialize a DiffBind object from the sample sheet containing all samples and peaks.
**Approach:** Read the sample sheet CSV into a DBA object that identifies overlapping peaks across samples.
```r
library(DiffBind)
## From sample sheet
dba_obj <- dba(sampleSheet = 'samples.csv')
适用场景
- 适合在comparing ChIP-seq binding between conditions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
- peak-calling - Generate input peak files
- peak-annotation - Annotate differential peaks
- differential-expression - Compare with RNA-seq
- pathway-analysis - Functional enrichment
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