txcutr

DOI: 10.18129/B9.bioc.txcutr  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see txcutr.

Transcriptome CUTteR

Bioconductor version: 3.16

Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.

Author: Mervin Fansler [aut, cre]

Maintainer: Mervin Fansler <mef3005 at med.cornell.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("txcutr")

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("txcutr")

 

HTML	R Script	Introduction to txcutr
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, RNASeq, Sequencing, Software, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	AnnotationDbi, GenomicFeatures, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils
LinkingTo
Suggests	RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	txcutr_1.4.0.tar.gz
Windows Binary	txcutr_1.4.0.zip
macOS Binary (x86_64)	txcutr_1.4.0.tgz
macOS Binary (arm64)	txcutr_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/txcutr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/txcutr
Bioc Package Browser	https://code.bioconductor.org/browse/txcutr/
Package Short Url	https://bioconductor.org/packages/txcutr/
Package Downloads Report	Download Stats