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bioskills

Skill1 starsChanged 12 days agoMITView on GitHub

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.

1 other project uses a version of this, 1 of them edited.

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The file

We split this skill into the rules it gives an agent

2 rules. About 0 are common, 1 is distinctive, and 1 is very specific to this project.

  • ≈0

    Common · estimate

    Many files like this have a rule of this kind.

  • ≈1

    Distinctive · estimate

    This author's own choices. Worth a look.

  • 1

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Distinctive:

    Run the bundled install script to download and install all bioSkills:

    line 14
  2. Very specific:

    After installation, 425 individual skills become available across these categories: sequence-io, sequence-manipulation, database-access, …

    line 66

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
SKILL.md

运行依赖:需要本机已安装命令 git;缺失时先安装 / 配置,再执行正文步骤。

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 GroupCategoriesSkills
Sequence & Alignmentsequence-io, sequence-manipulation, alignment, alignment-files, database-access40
Read Processingread-qc, read-alignment11
RNA-seq & Expressiondifferential-expression, rna-quantification, expression-matrix14
Single-Cell & Spatialsingle-cell, spatial-transcriptomics25
Variant Analysisvariant-calling, copy-number, phasing-imputation21
Epigenomicschip-seq, atac-seq, methylation-analysis, hi-c-analysis25
Metagenomics & Microbiomemetagenomics, microbiome13
Genomics & Assemblygenome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design29
Regulatory & Causalgene-regulatory-networks, causal-genomics, rna-structure13
Temporal & Ecologicaltemporal-genomics, ecological-genomics11
Immunology & Clinicalimmunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics25
Specialized Omicsproteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy36
RNA Biologysmall-rna-seq, epitranscriptomics, clip-seq, ribo-seq20
Phylogenetics & Evolutionphylogenetics, population-genetics, comparative-genomics16
Structural & Systemsstructural-biology, systems-biology11
Screens & Cytometrycrispr-screens, flow-cytometry, imaging-mass-cytometry22
Pathway & Integrationpathway-analysis, multi-omics-integration, restriction-analysis14
Infrastructuredata-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing39
WorkflowsEnd-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

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