Package: transmogR 1.9.0

Stevie Pederson

transmogR: Modify a set of reference sequences using a set of variants

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.

Authors:Stevie Pederson [aut, cre]

transmogR_1.9.0.tar.gz
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transmogR_1.9.0.tgz(r-4.6-x86_64)transmogR_1.9.0.tgz(r-4.6-arm64)transmogR_1.9.0.tgz(r-4.5-x86_64)transmogR_1.9.0.tgz(r-4.5-arm64)
transmogR_1.9.0.tar.gz(r-4.7-arm64)transmogR_1.9.0.tar.gz(r-4.7-x86_64)transmogR_1.9.0.tar.gz(r-4.6-arm64)transmogR_1.9.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
transmogR/json (API)
NEWS

# Install 'transmogR' in R:

install.packages('transmogR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/smped/transmogr/issues

Uses libs:

zlib– Compression library

On BioConductor:transmogR-1.9.0(bioc 3.24)transmogR-1.8.0(bioc 3.23)

alignment genomicvariation sequencing transcriptomevariant variantannotation zlib

4.78 score 6 scripts 262 downloads 14 exports 81 dependencies

Last updated from:2035130cc4. Checks:12 NOTE, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	256
linux-devel-arm64	NOTE	411
linux-devel-x86_64	NOTE	528
source / vignettes	OK	512
linux-release-arm64	NOTE	415
linux-release-x86_64	NOTE	545
macos-release-arm64	NOTE	300
macos-release-x86_64	NOTE	803
macos-oldrel-arm64	NOTE	309
macos-oldrel-x86_64	NOTE	814
windows-devel	NOTE	418
windows-release	NOTE	334
windows-oldrel	NOTE	424
wasm-release	FAIL	210

Exports:cleanVariants digestSalmon genomogrify indelcator overdispFromBoots overlapsByVar owl parY shiftByVar sjFromExons transmogrify upsetVarByCol varTags varTypes

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl patchwork pkgconfig png R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SummarizedExperiment sys VariantAnnotation vctrs viridisLite withr XML XVector yaml

Creating a Variant-Modified Reference

Stevie Pederson

Rendered fromcreating_a_new_reference.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-03
Started: 2024-01-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check provided variants for compatibility	cleanVariants cleanVariants,GRanges-method cleanVariants,VcfFile-method cleanVariants-methods
Parse the output from salmon	digestSalmon overdispFromBoots
Mogrify a genome using a set of variants	genomogrify genomogrify,BSgenome,GRanges-method genomogrify,BSgenome,VcfFile-method genomogrify,XStringSet,GRanges-method genomogrify,XStringSet,VcfFile-method genomogrify-methods
Substitute InDels into one or more sequences	indelcator indelcator,BSgenome,GRanges-method indelcator,DNAStringSet,GRanges-method indelcator,XString,GRanges-method
Count overlaps by variant type	overlapsByVar overlapsByVar,GRanges,GRanges-method overlapsByVar,GRangesList,GRanges-method overlapsByVar-methods
OverWrite Letters in an XStringSet	owl owl,BSgenome,GRanges-method owl,XStringSet,GRanges-method
Get the PAR-Y Regions From a Seqinfo Object	parY parY,character-method parY,Seqinfo-method parY-methods
Calculate new exon co-ordinates	shiftByVar
Obtain Splice-Junctions from Exons and Transcripts	sjFromExons
Mogrify a transcriptome using a set of variants	transmogrify transmogrify,BSgenome,GRanges,GRanges-method transmogrify,BSgenome,VcfFile,GRanges-method transmogrify,XStringSet,GRanges,GRanges-method transmogrify,XStringSet,VcfFile,GRanges-method transmogrify-methods
Show Variants by Impacted Columns	upsetVarByCol
Create a set of tags indicating overlap status with variants	varTags
Identify SNVs, Insertions and Deletions	varTypes