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This is the development version of transmogR; for the stable release version, see transmogR.

Modify a set of reference sequences using a set of variants

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 1.1.0
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_1.1.0.tar.gz
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macOS Binary (x86_64) transmogR_1.1.0.tgz
macOS Binary (arm64) transmogR_1.1.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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