chromatin-state-inference
This skill should be used when users need to infer chromatin states from histone modification ChIP-seq data using chromHMM. It provides workflows for chromatin state segmentation, model training, state annotation.
npx skills add majiayu000/claude-skill-registry --skill 15-chromatin-state-inference --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# ChromHMM Chromatin State Inference ## Overview This skill enables comprehensive chromatin state analysis using chromHMM for histone modification ChIP-seq data. ChromHMM uses a multivariate Hidden Markov Model to segment the genome into discrete chromatin states based on combinatorial patterns of histone modifications. Main steps include: - Refer to **Inputs & Outputs** to verify necessary files. - **Always prompt user** if required files are missing. - **Always prompt user** for genome assembly used. - **Always prompt user** for the bin size for generating binarized files. - **Always prompt user** for the bin size for the number of states the ChromHMM target. - **Always prompt user** for the absolute path of ChromHMM JAR file. - **Run chromHMM workflow**: Binarization → Learning. --- ## When to use this skill Use this skill when you need to infer chromatin states from histone modification ChIP-seq data using chromHMM. --- ## Inputs & Outputs ### Inputs (1) Option 1: BED files of aligned reads ```bash <mark1>.bed <mark2>.bed ... # Other marks ``` (1) Option 2: BAM files of aligned reads ```bash <mark1>.bam <mark2>.bam ... # Other marks ``` ### Outputs ```bash chromhmm_output/ bina
- Overview
- When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 1: Prepare the cellmarkfile
- Step 2: Data Binarization
- Step 3: Model Learning
- Parameter Optimization
- Number of States
- Bin Size
- State Interpretation
- Common Chromatin States
chromhmm_output/ binarized/ model/
What does the chromatin-state-inference skill do?
This skill should be used when users need to infer chromatin states from histone modification ChIP-seq data using chromHMM. It provides workflows for chromatin state segmentation, model training, state annotation.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 15-chromatin-state-inference --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.