alterlab-deeptools
byalterlab-ieu· 90 skills
Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/peak heatmaps and profiles (computeMatrix, plotHeatmap, plotProfile). Use for coverage tracks, signal heatmaps/profiles, normalization (RPGC/CPM/RPKM), and effective-genome-size lookups for ChIP-seq, ATAC-seq, MNase-seq, or RNA-seq. NOT for per-read/CIGAR/MAPQ BAM record access — that is pysam. Part of the AlterLab Academic Skills suite.
How to install alterlab-deeptools?
alterlab-ieu/alterlab-academic-skills/alterlab-deeptools
$npx -y skills add alterlab-ieu/alterlab-academic-skills --skill alterlab-deeptoolsInstalls into the current project.
›Prefer a prompt? Paste this to your agent
Run `npx skills use "https://github.com/alterlab-ieu/alterlab-academic-skills" --skill "alterlab-ieu/alterlab-academic-skills/alterlab-deeptools"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/alterlab-ieu/alterlab-academic-skills" that are relevant to the current task. Run `npx skills add "https://github.com/alterlab-ieu/alterlab-academic-skills"` and select the relevant skills, then follow their instructions.
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