transmogR
Modify a set of reference sequences using a set of variants
Bioconductor version: Release (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 <stephen.pederson.au at gmail.com>
citation("transmogR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("transmogR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("transmogR")| Creating a Variant-Modified Reference | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, GenomicVariation, Sequencing, Software, TranscriptomeVariant |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| License | GPL-3 |
| Depends | Biostrings, GenomicRanges |
| Imports | BSgenome, dplyr, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, jsonlite, matrixStats, methods, parallel, rlang, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation, vroom |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | transmogR_1.2.0.tar.gz |
| Windows Binary (x86_64) | transmogR_1.2.0.zip |
| macOS Binary (x86_64) | transmogR_1.2.0.tgz |
| macOS Binary (arm64) | transmogR_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/transmogR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/transmogR |
| Bioc Package Browser | https://code.bioconductor.org/browse/transmogR/ |
| Package Short Url | https://bioconductor.org/packages/transmogR/ |
| Package Downloads Report | Download Stats |