BioSkills
Verified@djemec
npx machina-cli add skill @djemec/bioskills --openclawbioSkills 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
Overview
bioSkills Installer is a meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for comprehensive bioinformatics analysis. It can install all skills at once or target specific categories, enabling rapid setup for RNA-seq, single-cell, variant calling, metagenomics, and more. Once installed, skills are automatically triggered by task requests such as differential expression or genome variant calling.
How This Skill Works
Run the bundled install script to download and install all bioSkills: bash scripts/install-bioskills.sh. Or install only specific categories with bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression". After installation, skills are automatically triggered based on the task at hand, allowing seamless end-to-end analysis from raw data to results.
When to Use It
- Starting a new bioinformatics project that requires broad coverage across multiple categories (e.g., sequence analysis through epigenomics).
- You need a specialized skill that isn’t yet installed and want to add it without reinstalling everything.
- You want to install only specific categories to save time and disk space (e.g., single-cell, differential expression, variant calling).
- Setting up end-to-end pipelines from FASTQ to results for streamlined workflows.
- You want tasks like RNA-seq differential expression, variant calling from WGS BAMs, scRNA-seq clustering, or metagenomics classification to trigger automatically.
Quick Start
- Step 1: Ensure prerequisites are available (git, and optionally python3 and Rscript) on macOS or Linux.
- Step 2: Install all bioSkills: bash scripts/install-bioskills.sh
- Step 3: If you need only certain categories, install them with: bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression"
Best Practices
- Verify prerequisites: ensure git is installed and your environment exposes python3 and/or Rscript if needed.
- Choose installation scope wisely: full installation for broad coverage or category-specific install to conserve resources.
- Run from a stable project environment to keep bioskills consistent across teammates.
- Test with example requests (e.g., differential-expression, variant-calling) after installation to confirm functionality.
- Keep bioSkills up to date by re-running the installer when updates are released.
Example Use Cases
- 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.
