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