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

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DOI: 10.18129/B9.bioc.transmogR

Bioconductor version: Release (3.22)

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 iD 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")

Creating a Variant-Modified Reference HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, GenomicVariation, Sequencing, Software, TranscriptomeVariant, VariantAnnotation

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License GPL-3

Depends R (>= 4.1.0), Biostrings, GenomicRanges

Imports BSgenome, data.table, Seqinfo, GenomicFeatures, ggplot2 (>= 4.0.0), IRanges, jsonlite, matrixStats, methods, parallel, patchwork, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation

System Requirements

URL https://github.com/smped/transmogR

Bug Reports https://github.com/smped/transmogR/issues

Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, edgeR, extraChIPs, InteractionSet, knitr, readr, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0)

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Package Archives

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

Source Package transmogR_1.6.0.tar.gz

Windows Binary (x86_64) transmogR_1.5.1.zip

macOS Binary (x86_64) transmogR_1.6.0.tgz

macOS Binary (arm64) transmogR_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/transmogR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/transmogR

Bioc Package Browser https://code.bioconductor.org/browse/transmogR/

Package Short Url https://bioconductor.org/packages/transmogR/

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