txcutr
This is the development version of txcutr; for the stable release version, see txcutr.
Transcriptome CUTteR
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Mervin Fansler <fanslerm at mskcc.org>
citation("txcutr")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")| Introduction to txcutr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils |
| System Requirements | |
| URL |
See More
| Suggests | RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 |
| 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 | txcutr_1.13.0.tar.gz |
| Windows Binary (x86_64) | txcutr_1.13.0.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |