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transmogR

This is the development version of transmogR; to use it, please install the devel version of Bioconductor.

Modify a set of reference sequences using a set of variants


Bioconductor version: Development (3.19)

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]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, GenomicVariation, Sequencing, Software, TranscriptomeVariant
Version 0.99.5
In Bioconductor since BioC 3.19 (R-4.4)
License GPL-3
Depends Biostrings, GenomicRanges
Imports BSgenome, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, 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, extraChIPs, InteractionSet, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package transmogR_0.99.5.tar.gz
Windows Binary transmogR_0.99.5.zip
macOS Binary (x86_64) transmogR_0.99.5.tgz
macOS Binary (arm64) transmogR_0.99.5.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/
Package Downloads Report Download Stats