huang-sh/deepscience/bioskills

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

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