skills/claude-scientific-skills
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Add pysam

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Timothy Kassis
2025-10-20 19:02:16 -07:00
parent 86243b1c45
commit 50b1b5e607
8 changed files with 1846 additions and 3 deletions
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@@ -54,6 +54,7 @@ After installing the plugin, you can use the skill by just mentioning it. Additi
- **BioServices** - Programmatic access to 40+ biological web services (KEGG, UniProt, ChEBI, ChEMBL)
- **Cellxgene Census** - Query and analyze large-scale single-cell RNA-seq data
- **gget** - Efficient genomic database queries (Ensembl, UniProt, NCBI, PDB, COSMIC)
- **pysam** - Read, write, and manipulate genomic data files (SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences) with pileup analysis, coverage calculations, and bioinformatics workflows
- **PyDESeq2** - Differential gene expression analysis for bulk RNA-seq data
- **Scanpy** - Single-cell RNA-seq analysis with clustering, marker genes, and UMAP/t-SNE visualization
@@ -137,7 +138,6 @@ After installing the plugin, you can use the skill by just mentioning it. Additi
- **WikiPathways** - Community-curated biological pathway database
### Bioinformatics & Genomics
- **pysam** - Interface to SAM/BAM/CRAM format files
- **pybedtools** - Wrapper for BEDTools genome arithmetic operations
- **mygene** - Python client for MyGene.Info gene query service
- **pyensembl** - Python interface to Ensembl reference genome metadata