bioskills

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.
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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 scripts/install-bioskills.sh

Or install only specific categories:

bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression"

What Gets Installed

Category Group	Categories	Skills
Sequence & Alignment	sequence-io, sequence-manipulation, alignment, alignment-files, database-access	40
Read Processing	read-qc, read-alignment	11
RNA-seq & Expression	differential-expression, rna-quantification, expression-matrix	14
Single-Cell & Spatial	single-cell, spatial-transcriptomics	25
Variant Analysis	variant-calling, copy-number, phasing-imputation	21
Epigenomics	chip-seq, atac-seq, methylation-analysis, hi-c-analysis	25
Metagenomics & Microbiome	metagenomics, microbiome	13
Genomics & Assembly	genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design	29
Regulatory & Causal	gene-regulatory-networks, causal-genomics, rna-structure	13
Temporal & Ecological	temporal-genomics, ecological-genomics	11
Immunology & Clinical	immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics	25
Specialized Omics	proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy	36
RNA Biology	small-rna-seq, epitranscriptomics, clip-seq, ribo-seq	20
Phylogenetics & Evolution	phylogenetics, population-genetics, comparative-genomics	16
Structural & Systems	structural-biology, systems-biology	11
Screens & Cytometry	crispr-screens, flow-cytometry, imaging-mass-cytometry	22
Pathway & Integration	pathway-analysis, multi-omics-integration, restriction-analysis	14
Infrastructure	data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing	39
Workflows	End-to-end pipelines (FASTQ to results)	40

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

Related Skills

After installation, 425 individual skills become available across these categories: sequence-io, sequence-manipulation, database-access, alignment, alignment-files, variant-calling, phylogenetics, differential-expression, structural-biology, single-cell, pathway-analysis, restriction-analysis, methylation-analysis, chip-seq, metagenomics, long-read-sequencing, read-qc, read-alignment, rna-quantification, genome-assembly, genome-intervals, data-visualization, expression-matrix, copy-number, proteomics, flow-cytometry, population-genetics, multi-omics-integration, spatial-transcriptomics, machine-learning, workflow-management, microbiome, metabolomics, phasing-imputation, primer-design, hi-c-analysis, imaging-mass-cytometry, atac-seq, crispr-screens, reporting, experimental-design, clinical-databases, tcr-bcr-analysis, small-rna-seq, epitranscriptomics, clip-seq, ribo-seq, genome-engineering, systems-biology, epidemiological-genomics, immunoinformatics, comparative-genomics, alternative-splicing, chemoinformatics, liquid-biopsy, genome-annotation, gene-regulatory-networks, causal-genomics, rna-structure, temporal-genomics, ecological-genomics, workflows