transmogR
This is the released version of transmogR; for the devel version, see transmogR.
Modify a set of reference sequences using a set of variants
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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, VariantAnnotation |
| Version | 1.8.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0), Biostrings, GenomicRanges |
| Imports | BSgenome, data.table, Seqinfo, GenomicFeatures, ggplot2 (>= 4.0.0), IRanges, jsonlite, matrixStats, methods, parallel, patchwork, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation |
| System Requirements | |
| URL | https://github.com/smped/transmogR |
| Bug Reports | https://github.com/smped/transmogR/issues |
See More
| Suggests | BiocStyle, BSgenome.Hsapiens.UCSC.hg38, edgeR, extraChIPs, InteractionSet, knitr, readr, rmarkdown, rtracklayer, SimpleUpset, 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_1.8.1.tar.gz |
| Windows Binary (x86_64) | transmogR_1.8.1.zip |
| macOS Binary (big-sur-x86_64) | transmogR_1.8.1.tgz |
| macOS Binary (sonoma-arm64) | transmogR_1.8.1.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 |
| Old Source Packages for BioC 3.23 | Source Archive |