bioc-howto

name	bioc-howto
description	A consolidated index of Bioconductor how-to skills covering genomics, sequencing, and omics data analysis tasks
version	1.0.0
category	bioconductor-how-tos
author	bioconductor

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