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 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
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
26| Category Group | Categories | Skills |
27|----------------|-----------|--------|
28| Sequence & Alignment | sequence-io, sequence-manipulation, alignment, alignment-files, database-access | 40 |
29| Read Processing | read-qc, read-alignment | 11 |
30| RNA-seq & Expression | differential-expression, rna-quantification, expression-matrix | 14 |
31| Single-Cell & Spatial | single-cell, spatial-transcriptomics | 25 |
32| Variant Analysis | variant-calling, copy-number, phasing-imputation | 21 |
33| Epigenomics | chip-seq, atac-seq, methylation-analysis, hi-c-analysis | 25 |
34| Metagenomics & Microbiome | metagenomics, microbiome | 13 |
35| Genomics & Assembly | genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design | 29 |
36| Regulatory & Causal | gene-regulatory-networks, causal-genomics, rna-structure | 13 |
37| Temporal & Ecological | temporal-genomics, ecological-genomics | 11 |
38| Immunology & Clinical | immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics | 25 |
39| Specialized Omics | proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy | 36 |
40| RNA Biology | small-rna-seq, epitranscriptomics, clip-seq, ribo-seq | 20 |
41| Phylogenetics & Evolution | phylogenetics, population-genetics, comparative-genomics | 16 |
42| Structural & Systems | structural-biology, systems-biology | 11 |
43| Screens & Cytometry | crispr-screens, flow-cytometry, imaging-mass-cytometry | 22 |
44| Pathway & Integration | pathway-analysis, multi-omics-integration, restriction-analysis | 14 |
45| Infrastructure | data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing | 39 |
46| Workflows | End-to-end pipelines (FASTQ to results) | 40 |
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
61
62## Related Skills
63
64After installation, 425 individual skills become available across these categories:
65sequence-io, sequence-manipulation, database-access, alignment, alignment-files,
66variant-calling, phylogenetics, differential-expression, structural-biology,
67single-cell, pathway-analysis, restriction-analysis, methylation-analysis,
68chip-seq, metagenomics, long-read-sequencing, read-qc, read-alignment,
69rna-quantification, genome-assembly, genome-intervals, data-visualization,
70expression-matrix, copy-number, proteomics, flow-cytometry, population-genetics,
71multi-omics-integration, spatial-transcriptomics, machine-learning,
72workflow-management, microbiome, metabolomics, phasing-imputation,
73primer-design, hi-c-analysis, imaging-mass-cytometry, atac-seq,
74crispr-screens, reporting, experimental-design, clinical-databases,
75tcr-bcr-analysis, small-rna-seq, epitranscriptomics, clip-seq, ribo-seq,
76genome-engineering, systems-biology, epidemiological-genomics,
77immunoinformatics, comparative-genomics, alternative-splicing,
78chemoinformatics, liquid-biopsy, genome-annotation, gene-regulatory-networks,
79causal-genomics, rna-structure, temporal-genomics, ecological-genomics, workflows
modbender