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Modify a set of reference sequences using a set of variants

Bioconductor version: Release (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 < at>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

Creating a Variant-Modified Reference HTML R Script
Reference Manual PDF


biocViews Alignment, GenomicVariation, Sequencing, Software, TranscriptomeVariant
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
Depends Biostrings, GenomicRanges
Imports BSgenome, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, methods, parallel, rlang, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation
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Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, extraChIPs, InteractionSet, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package transmogR_1.0.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) transmogR_1.0.0.tgz
macOS Binary (arm64) transmogR_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive