txcutr

DOI: 10.18129/B9.bioc.txcutr    

This is the development version of txcutr; for the stable release version, see txcutr.

Transcriptome CUTteR

Bioconductor version: Development (3.15)

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>

Citation (from within R, enter citation("txcutr")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) txcutr_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/txcutr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/txcutr
Package Short Url https://bioconductor.org/packages/txcutr/
Package Downloads Report Download Stats

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