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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

Reference Manual PDF

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)
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/transmogR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/transmogR
Package Short Url https://bioconductor.org/packages/transmogR/
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