bioinformatics-installer
Skill20 starsChanged 8 months agoAGPL-3.0View on GitHub
Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts, and Python requirements. Use when the user needs to set up a bioinformatics workstation, install tools for a specific assay, create reproducible environments, or troubleshoot dependency issues. Trigger on: install tools, set up environment, conda create, bioinformatics setup, install R packages, install Bioconductor, install pipeline tools.
- Installs packages
In this repository46 other files it gives its agents.
- accessibility-aggregationSkill
- batch-analysisSkill
- cellxgene-contextSkill
- cite-encodeSkill
- clinvar-annotationSkill
- compare-biosamplesSkill
- cross-referenceSkill
- data-provenanceSkill
- disease-researchSkill
- download-encodeSkill
- ensembl-annotationSkill
- epigenome-profilingSkill
- functional-screen-analysisSkill
- geo-connectorSkill
- gnomad-variantsSkill
- gtex-expressionSkill
- gwas-catalogSkill
- hic-aggregationSkill
- histone-aggregationSkill
- integrative-analysisSkill
- jaspar-motifsSkill
- liftover-coordinatesSkill
- methylation-aggregationSkill
- motif-analysisSkill
- multi-omics-integrationSkill
- peak-annotationSkill
- pipeline-atacseqSkill
- pipeline-chipseqSkill
- pipeline-cutandrunSkill
- pipeline-dnaseseqSkill
- pipeline-guideSkill
- pipeline-hicSkill
- pipeline-rnaseqSkill
- pipeline-wgbsSkill
- publication-trustSkill
- quality-assessmentSkill
- regulatory-elementsSkill
- scientific-writingSkill
- scrna-meta-analysisSkill
- search-encodeSkill
- setupSkill
- single-cell-encodeSkill
- track-experimentsSkill
- ucsc-browserSkill
- variant-annotationSkill
- visualization-workflowSkill
The file
We split this skill into the rules it gives an agent
4 rules. About 0 are common, 2 are distinctive, and 2 are very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈2
Distinctive · estimate
This author's own choices. Worth a look.
2
Very specific
Tied to their project's names, files or tools. Probably skip.
Licensed with conditions — read it at the source. We count its rules but don't quote them. Read them on GitHub.
≈ “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.
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