deeptools-ngs-analysis
NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.
npx skills add BioTender-max/awesome-bio-agent-skills --skill deeptools-ngs-analysis --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.
# deepTools — NGS Data Analysis Toolkit ## Overview deepTools is a command-line toolkit for processing and visualizing high-throughput sequencing data. It converts BAM alignments to normalized coverage tracks (bigWig), performs quality control (correlation, PCA, fingerprint), and generates publication-quality heatmaps and profile plots around genomic features. Supports ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq. ## When to Use - Converting BAM files to normalized bigWig coverage tracks - Comparing ChIP-seq treatment vs input control (log2 ratio tracks) - Assessing sample quality: replicate correlation, PCA, coverage depth - Evaluating ChIP enrichment strength (fingerprint plots) - Creating heatmaps and profile plots around TSS, peaks, or other genomic regions - Analyzing ATAC-seq data with Tn5 offset correction - Generating strand-specific RNA-seq coverage tracks - For **read alignment**, use STAR, BWA, or bowtie2 instead - For **peak calling**, use MACS2 or HOMER instead - For **BAM/VCF file manipulation**, use pysam instead ## Prerequisites ```bash pip install deeptools # Verify installation bamCoverage --version ``` **Input requirements**: BAM files must be sorted and indexed (`
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- 1. BAM to Coverage Conversion
- 2. Sample Comparison
- 3. Quality Control
- 4. Heatmaps and Profile Plots
- 5. Read Filtering and Processing
- 6. Enrichment Analysis
- Key Concepts
- Normalization Methods
- Effective Genome Sizes
pip install deeptools Verify installation bamCoverage --version Convert BAM to normalized bigWig bamCoverage --bam sample.bam --outFileName sample.bw \ Create heatmap around TSS computeMatrix reference-point -S sample.bw -R genes.bed \ plotHeatmap -m matrix.gz -o heatmap.png --colorMap RdBu Basic conversion with RPGC normalization bamCoverage --bam input.bam --outFileName output.bw \
What does the deeptools-ngs-analysis skill do?
NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill deeptools-ngs-analysis --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 BioTender-max/awesome-bio-agent-skills, a repository with 144 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.