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Transcriptome CUTteR

Bioconductor version: Release (3.19)

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 <fanslerm at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to txcutr HTML R Script
Reference Manual PDF


biocViews Alignment, Annotation, RNASeq, Sequencing, Software, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
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Suggests RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3
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Follow Installation instructions to use this package in your R session.

Source Package txcutr_1.10.0.tar.gz
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macOS Binary (x86_64) txcutr_1.10.0.tgz
macOS Binary (arm64) txcutr_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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