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Bioconductor - transmogR

transmogR

This is the released version of transmogR; for the devel version, see transmogR.

Modify a set of reference sequences using a set of variants

Bioconductor version: Release (3.21)

transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.

Author: Stevie Pederson [aut, cre] ORCID: 0000-0001-8197-3303

Maintainer: Stevie Pederson <stephen.pederson.au at gmail.com>

Citation (from within R, enter citation("transmogR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("transmogR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("transmogR")
Details biocViews Alignment, GenomicVariation, Sequencing, Software, TranscriptomeVariant, VariantAnnotation Version 1.4.1 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License GPL-3 Depends R (>= 4.1.0), Biostrings, GenomicRanges Imports BSgenome, data.table, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, jsonlite, matrixStats, methods, parallel, rlang, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation System Requirements URL https://github.com/smped/transmogR Bug Reports https://github.com/smped/transmogR/issues See More Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, edgeR, extraChIPs, InteractionSet, knitr, readr, rmarkdown, rtracklayer, testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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