Check Requirements for Transcriptome Extraction from GTF

Source: R/validate.R

Verifies that all packages needed to extract a transcriptome FASTA from a GTF annotation file are available.

require_transcriptome_extraction()

Value

Invisible TRUE if all requirements are met

Details

Extracting a transcriptome from a genome reference (BSgenome) and GTF annotation requires these Bioconductor packages:

  • Biostrings: For sequence manipulation

  • rtracklayer: To parse GTF annotation files

  • GenomicRanges: For genomic coordinate operations

  • BSgenome: To access genome sequences

Installation

If any package is missing, install with:

BiocManager::install(c("Biostrings", "rtracklayer", "GenomicRanges", "BSgenome"))

Examples

if (FALSE) { # \dontrun{
# Check before using GTF -> FASTA extraction
require_transcriptome_extraction()
} # }