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
1---2name: bioskills3description: 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.4---5
6# bioSkills Installer
7
8Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for bioinformatics analysis.
9
10## Installation
11
12Run the bundled install script to download and install all bioSkills:
13
14```bash
15bash scripts/install-bioskills.sh
16```
17
18Or install only specific categories:
19
20```bash
21bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression"
22```
23
24## What Gets Installed
25
26425 skills across 62 categories covering:
27
28- **Sequence & Alignment** (40): sequence-io, sequence-manipulation, alignment, alignment-files, database-access
29- **Read Processing** (11): read-qc, read-alignment
30- **RNA-seq & Expression** (14): differential-expression, rna-quantification, expression-matrix
31- **Single-Cell & Spatial** (25): single-cell, spatial-transcriptomics
32- **Variant Analysis** (21): variant-calling, copy-number, phasing-imputation
33- **Epigenomics** (25): chip-seq, atac-seq, methylation-analysis, hi-c-analysis
34- **Metagenomics & Microbiome** (13): metagenomics, microbiome
35- **Genomics & Assembly** (29): genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design
36- **Regulatory & Causal** (13): gene-regulatory-networks, causal-genomics, rna-structure
37- **Temporal & Ecological** (11): temporal-genomics, ecological-genomics
38- **Immunology & Clinical** (25): immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics
39- **Specialized Omics** (36): proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy
40- **RNA Biology** (20): small-rna-seq, epitranscriptomics, clip-seq, ribo-seq
41- **Phylogenetics & Evolution** (16): phylogenetics, population-genetics, comparative-genomics
42- **Structural & Systems** (11): structural-biology, systems-biology
43- **Screens & Cytometry** (22): crispr-screens, flow-cytometry, imaging-mass-cytometry
44- **Pathway & Integration** (14): pathway-analysis, multi-omics-integration, restriction-analysis
45- **Infrastructure** (39): data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing
46- **Workflows** (40): end-to-end pipelines (FASTQ to results)
47
48## After Installation
49
50Once installed, skills are automatically triggered based on the task at hand. Example requests:
51
52- "I have RNA-seq counts from treated vs control samples - find the differentially expressed genes"
53- "Call variants from this whole genome sequencing BAM file"
54- "Cluster my single-cell RNA-seq data and find marker genes"
55- "Predict the structure of this protein sequence"
56- "Run a metagenomics classification on these shotgun reads"
57
58## Source
59
60GitHub: https://github.com/GPTomics/bioSkills
gabrielmoreira