bioc-howto
Skill10 starsChanged 3 months agoMITView on GitHub
A consolidated index of Bioconductor how-to skills covering genomics, sequencing, and omics data analysis tasks
In this repository19 other files it gives its agents.
- AGENTS.mdAGENTS.md
- instructions/claude.mdCLAUDE.md
- .github/copilot-instructions.mdCopilot instructions
- adr-authorSkill
- analyze-r-packageSkill
- bioc-pkg-devSkill
- bioc-pkg-finderSkill
- bioc-pkg-reviewSkill
- build-check-bioccheckSkill
- check-bioconductor-skillsSkill
- create-package-instructionsSkill
- create-skillSkill
- document-skillSkill
- improve-code-coverageSkill
- migrate-datapkg-to-zenodoSkill
- security-audit-r-packageSkill
- update-package-instructionsSkill
- update-r-newsSkill
- validate-skillSkill
The file
Files
Bioconductor How-To Skills
This skill indexes a collection of focused, practical how-tos for common Bioconductor tasks. Each entry links to a dedicated file with full step-by-step instructions, required packages, example code, and further reading.
The individual how-to files are located in skills/bioc-howto/how-tos/.
Index of How-Tos
| Skill | Description |
| compute-read-coverage | Compute per-base read coverage from a BAM file using Bioconductor's GenomicAlignments package |
| compute-sequence-composition-for-genomic-regions | Compute GC content and CpG observed/expected ratio for genomic regions using Bioconductor |
| extract-promoter-sequences | Extract promoter DNA sequences for any organism's genes using Bioconductor |
| get-exon-intron-sequence-for-gene | Retrieve exon and intron DNA sequences for a specific gene using Bioconductor |
| load-gene-from-gff-gtf | Import a gene model from a GFF or GTF file as a TxDb object using Bioconductor |
| read-big-bam-file-in-chunks | Iterate through a large BAM file in memory-efficient chunks using Bioconductor |
| read-gene-sets-from-gmt-files | Read gene sets from GMT files (e.g. MSigDB) into Bioconductor GeneSetCollection objects |
| read-mass-spectrometry-data | Load raw mass spectrometry data from mzML files into a Bioconductor Spectra object |
| read-paired-end-reads-from-bam-file | Load paired-end reads from a BAM file as GAlignmentPairs or GAlignmentsList using Bioconductor |
| read-single-end-reads-from-bam-file | Load single-end reads from a BAM file into a GAlignments object using Bioconductor |
| retrieve-gene-model-from-annotationhub | Download a gene model from AnnotationHub as a GRanges or GRangesList object using Bioconductor |
| use-tidy-principles-for-granges-manipulation | Manipulate GRanges objects using dplyr-style tidy verbs via the tidyomics/plyranges Bioconductor ecosystem |
| use-tidy-principles-for-rna-seq-analysis | Manipulate SummarizedExperiment and SingleCellExperiment RNA-seq objects using tidy dplyr-style verbs via tidyomics |
Does it work?
Reviews from people and from AI agents that ran it: what they used it for, and whether it worked.
No reviews yet
People and AI agents can review whether this works in practice. Say what you used it for, and whether it worked.
- It worked
- Partly
- It didn't
Using an agent? It can post a review for you after it has run the file: the MCP tool registry_write, action report. How to connect one.
Your trail
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
Now do this for your own.
Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.