bioskills-installer
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How to install bioskills-installer?
gptomics/bioskills/bioskills-installer
$npx -y skills add GPTomics/bioSkills --skill bioskills-installerInstalls 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 instal
SKILL.md
| 1 | # bioSkills Installer |
| 2 | |
| 3 | Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for bioinformatics analysis. |
| 4 | |
| 5 | ## Installation |
| 6 | |
| 7 | Run the bundled install script to download and install all bioSkills: |
| 8 | |
| 9 | ```bash |
| 10 | bash scripts/install-bioskills.sh |
| 11 | ``` |
| 12 | |
| 13 | Or install only specific categories: |
| 14 | |
| 15 | ```bash |
| 16 | bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression" |
| 17 | ``` |
| 18 | |
| 19 | ## What Gets Installed |
| 20 | |
| 21 | 425 skills across 62 categories covering: |
| 22 | |
| 23 | - **Sequence & Alignment** (40): sequence-io, sequence-manipulation, alignment, alignment-files, database-access |
| 24 | - **Read Processing** (11): read-qc, read-alignment |
| 25 | - **RNA-seq & Expression** (14): differential-expression, rna-quantification, expression-matrix |
| 26 | - **Single-Cell & Spatial** (25): single-cell, spatial-transcriptomics |
| 27 | - **Variant Analysis** (21): variant-calling, copy-number, phasing-imputation |
| 28 | - **Epigenomics** (25): chip-seq, atac-seq, methylation-analysis, hi-c-analysis |
| 29 | - **Metagenomics & Microbiome** (13): metagenomics, microbiome |
| 30 | - **Genomics & Assembly** (29): genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design |
| 31 | - **Regulatory & Causal** (13): gene-regulatory-networks, causal-genomics, rna-structure |
| 32 | - **Temporal & Ecological** (11): temporal-genomics, ecological-genomics |
| 33 | - **Immunology & Clinical** (25): immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics |
| 34 | - **Specialized Omics** (36): proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy |
| 35 | - **RNA Biology** (20): small-rna-seq, epitranscriptomics, clip-seq, ribo-seq |
| 36 | - **Phylogenetics & Evolution** (16): phylogenetics, population-genetics, comparative-genomics |
| 37 | - **Structural & Systems** (11): structural-biology, systems-biology |
| 38 | - **Screens & Cytometry** (22): crispr-screens, flow-cytometry, imaging-mass-cytometry |
| 39 | - **Pathway & Integration** (14): pathway-analysis, multi-omics-integration, restriction-analysis |
| 40 | - **Infrastructure** (39): data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing |
| 41 | - **Workflows** (40): end-to-end pipelines (FASTQ to results) |
| 42 | |
| 43 | ## After Installation |
| 44 | |
| 45 | Once installed, skills are automatically triggered based on the task at hand. Example requests: |
| 46 | |
| 47 | - "I have RNA-seq counts from treated vs control samples - find the differentially expressed genes" |
| 48 | - "Call variants from this whole genome sequencing BAM file" |
| 49 | - "Cluster my single-cell RNA-seq data and find marker genes" |
| 50 | - "Predict the structure of this protein sequence" |
| 51 | - "Run a metagenomics classification on these shotgun reads" |
| 52 | |
| 53 | ## Source |
| 54 | |
| 55 | GitHub: https://github.com/GPTomics/bioSkills |
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