bio-chipseq-differential-binding SKILL.md skillA
bio-chipseq-differential-binding from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-chipseq-differential-binding@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/bio-chipseq-differential-binding/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
- Size
- 7,540 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: DESeq2 1.42+, edgeR 4.0+
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
# Differential Binding with DiffBind
**"Compare ChIP-seq binding between conditions"** → Identify genomic regions with statistically significant differences in transcription factor or histone mark occupancy between experimental groups.
- R: `DiffBind::dba()` → `dba.count()` → `dba.contrast()` → `dba.analyze()`
## 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.
```r
# Create sample sheet as data frame or CSV
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'),
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-chipseq-differential-binding@sha256:7ff23ae489806a00The line at the top of this page pins the label git:20260517.81511a7, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_7bvigfshf3pfv27a)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on May 17, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (7540 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_7bvigfshf3pfv27a GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-chipseq-differential-binding GET https://markdownregistry.com/api/v1/blob/7ff23ae489806a00fc4cb3818749372141def58242a347fe08c1d677acb3c669
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
More from fridrichmethod/awesome-skills
Every file in fridrichmethod/awesome-skills