deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
- Version
- 2.0
- License
- BSD license
- Compatibility
- Requires Python 3.12+ and deepTools 4.0.0 (including pysam and pyBigWig); samtools for sorting/indexing workflows. Network needed only for installation or retrieving public input data.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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- Bash
Files
- skills/deeptools/SKILL.md
- skills/deeptools/SKILL_CN.md
- skills/deeptools/assets/quick_reference.md
- skills/deeptools/references/core_workflows.md
- skills/deeptools/references/effective_genome_sizes.md
- skills/deeptools/references/normalization_methods.md
- skills/deeptools/references/review.md
- skills/deeptools/references/tools_reference.md
- skills/deeptools/references/workflows.md
- skills/deeptools/scripts/validate_files.py
- skills/deeptools/scripts/workflow_generator.py
Every link opens the file at its source, pinned to the revision this page describes.