Description
deeptools is an agent skill for NGS data analysis with deepTools, a suite of Python command-line tools for processing and analysing high-throughput sequencing data. It is used for quality control, normalising data, comparing samples, and making publication-quality plots for ChIP-seq, RNA-seq, ATAC-seq, MNase-seq and other sequencing experiments. Its core capabilities include converting BAM alignments into normalised coverage tracks in bigWig or bedGraph format, quality control such as fingerprint, correlation and coverage checks, comparing samples and correlating them, and producing heatmaps and profile plots around genomic features like transcription start sites and peaks. It also covers enrichment analysis and visualisation of peak regions. The skill is for analysts who have aligned reads and want coverage tracks or a quality assessment before comparing samples or plotting signal at features. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs. Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.…
Highlights
- BAM to bigWig or bedGraph coverage tracks
- Fingerprint, correlation and coverage QC
- Sample comparison and correlation
- Heatmaps and profiles around TSS and peaks
- For ChIP-seq, RNA-seq, ATAC-seq and MNase-seq
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deeptools FAQ
What is deepTools?
A suite of Python command-line tools for processing and analysing high-throughput sequencing data.
Which experiments does it cover?
ChIP-seq, RNA-seq, ATAC-seq, MNase-seq and other NGS experiments.
What can it produce?
Normalised coverage tracks in bigWig or bedGraph, QC plots, sample correlations, and heatmaps or profiles around genomic features.
What quality checks does it run?
Fingerprint, correlation and coverage assessments, as the skill lists them.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill deeptools.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best deeptools alternatives?
Popular alternatives to deeptools include gget, biopython and bulk-rnaseq. See all deeptools alternatives