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>

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


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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
Suggests RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3
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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/
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