bioskills
$
npx mdskill add GPTomics/bioSkills/bioskillsInstalls 425 bioinformatics skills across 62 categories for advanced analysis
- Solves bioinformatics tasks requiring specialized tools not yet installed
- Requires git, and optionally python3 or Rscript for execution
- Chooses relevant skills based on task type and category requirements
- Delivers installed tools and ready-to-use workflows for immediate analysis
SKILL.md
.github/skills/bioskillsView on GitHub ↗
---
name: bioskills
description: "Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed."
metadata: {"openclaw":{"requires":{"bins":["git"],"anyBins":["python3","Rscript"]},"os":["darwin","linux"],"emoji":"🧬"}}
---
# bioSkills Installer
Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for bioinformatics analysis.
## Installation
Run the bundled install script to download and install all bioSkills:
```bash
bash scripts/install-bioskills.sh
```
Or install only specific categories:
```bash
bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression"
```
## What Gets Installed
425 skills across 62 categories covering:
- **Sequence & Alignment** (40): sequence-io, sequence-manipulation, alignment, alignment-files, database-access
- **Read Processing** (11): read-qc, read-alignment
- **RNA-seq & Expression** (14): differential-expression, rna-quantification, expression-matrix
- **Single-Cell & Spatial** (25): single-cell, spatial-transcriptomics
- **Variant Analysis** (21): variant-calling, copy-number, phasing-imputation
- **Epigenomics** (25): chip-seq, atac-seq, methylation-analysis, hi-c-analysis
- **Metagenomics & Microbiome** (13): metagenomics, microbiome
- **Genomics & Assembly** (29): genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design
- **Regulatory & Causal** (13): gene-regulatory-networks, causal-genomics, rna-structure
- **Temporal & Ecological** (11): temporal-genomics, ecological-genomics
- **Immunology & Clinical** (25): immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics
- **Specialized Omics** (36): proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy
- **RNA Biology** (20): small-rna-seq, epitranscriptomics, clip-seq, ribo-seq
- **Phylogenetics & Evolution** (16): phylogenetics, population-genetics, comparative-genomics
- **Structural & Systems** (11): structural-biology, systems-biology
- **Screens & Cytometry** (22): crispr-screens, flow-cytometry, imaging-mass-cytometry
- **Pathway & Integration** (14): pathway-analysis, multi-omics-integration, restriction-analysis
- **Infrastructure** (39): data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing
- **Workflows** (40): end-to-end pipelines (FASTQ to results)
## After Installation
Once installed, skills are automatically triggered based on the task at hand. Example requests:
- "I have RNA-seq counts from treated vs control samples - find the differentially expressed genes"
- "Call variants from this whole genome sequencing BAM file"
- "Cluster my single-cell RNA-seq data and find marker genes"
- "Predict the structure of this protein sequence"
- "Run a metagenomics classification on these shotgun reads"
## Source
GitHub: https://github.com/GPTomics/bioSkills
More from GPTomics/bioSkills
- bio-admet-predictionPredicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering compounds for drug-likeness or prioritizing leads by predicted safety.
- bio-alignment-amplicon-clippingTrim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
- bio-alignment-filteringFilter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
- bio-alignment-indexingCreate and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
- bio-alignment-ioRead, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
- bio-alignment-msa-parsingParse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
- bio-alignment-msa-statisticsCalculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
- bio-alignment-multiplePerform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
- bio-alignment-pairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
- bio-alignment-sortingSort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.