How do I install the Bioc Howto skill?

Run npx skillmds@latest add bioconductor/bioc-howto in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Bioc Howto free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Bioc Howto?

Bioconductor (@bioconductor) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bioc Howto by bioconductor — Agent Skill

Name: Bioc Howto
Author: Bioconductor

File contents

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

---name: bioc-howtodescription: A consolidated index of Bioconductor how-to skills covering genomics, sequencing, and omics data analysis tasks---# Bioconductor How-To SkillsThis 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](how-tos/compute-read-coverage.md) | Compute per-base read coverage from a BAM file using Bioconductor's GenomicAlignments package || [compute-sequence-composition-for-genomic-regions](how-tos/compute-sequence-composition-for-genomic-regions.md) | Compute GC content and CpG observed/expected ratio for genomic regions using Bioconductor || [extract-promoter-sequences](how-tos/extract-promoter-sequences.md) | Extract promoter DNA sequences for any organism's genes using Bioconductor || [get-exon-intron-sequence-for-gene](how-tos/get-exon-intron-sequence-for-gene.md) | Retrieve exon and intron DNA sequences for a specific gene using Bioconductor || [load-gene-from-gff-gtf](how-tos/load-gene-from-gff-gtf.md) | Import a gene model from a GFF or GTF file as a TxDb object using Bioconductor || [read-big-bam-file-in-chunks](how-tos/read-big-bam-file-in-chunks.md) | Iterate through a large BAM file in memory-efficient chunks using Bioconductor || [read-gene-sets-from-gmt-files](how-tos/read-gene-sets-from-gmt-files.md) | Read gene sets from GMT files (e.g. MSigDB) into Bioconductor GeneSetCollection objects || [read-mass-spectrometry-data](how-tos/read-mass-spectrometry-data.md) | Load raw mass spectrometry data from mzML files into a Bioconductor Spectra object || [read-paired-end-reads-from-bam-file](how-tos/read-paired-end-reads-from-bam-file.md) | Load paired-end reads from a BAM file as GAlignmentPairs or GAlignmentsList using Bioconductor || [read-single-end-reads-from-bam-file](how-tos/read-single-end-reads-from-bam-file.md) | Load single-end reads from a BAM file into a GAlignments object using Bioconductor || [retrieve-gene-model-from-annotationhub](how-tos/retrieve-gene-model-from-annotationhub.md) | Download a gene model from AnnotationHub as a GRanges or GRangesList object using Bioconductor || [use-tidy-principles-for-granges-manipulation](how-tos/use-tidy-principles-for-granges-manipulation.md) | Manipulate GRanges objects using dplyr-style tidy verbs via the tidyomics/plyranges Bioconductor ecosystem || [use-tidy-principles-for-rna-seq-analysis](how-tos/use-tidy-principles-for-rna-seq-analysis.md) | Manipulate SummarizedExperiment and SingleCellExperiment RNA-seq objects using tidy dplyr-style verbs via tidyomics |

Frequently asked questions

Bioc Howto