Package: transmogR 1.1.0

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]

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transmogR.pdf |transmogR.html✨
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

On BioConductor:transmogR-1.1.0(bioc 3.20)transmogR-1.0.0(bioc 3.19)

bioconductor-package

9 exports 1.24 score 89 dependencies

Last updated 2 months agofrom:ba33d38a26

Exports:genomogrify indelcator overlapsByVar owl parY sjFromExons transmogrify upsetVarByCol varTypes

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon curl DBI DelayedArray fansi farver fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml zlibbioc

Creating a Variant-Modified Reference

Stevie Pederson

Rendered fromcreating_a_new_reference.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2024-04-05
Started: 2024-01-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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
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
Identify SNVs, Insertions and Deletions	varTypes