txcutr

Overview

Various mRNA sequencing library preparation methods generate sequencing reads from the transcript ends. Quantification of isoform usage can be improved by using truncated versions of transcriptome annotations when assigning such reads to isoforms. The txcutr package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.

Installation instructions

Bioconductor

Get the latest stable R release from CRAN. Then install txcutr using from Bioconductor the following code:

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

BiocManager::install("txcutr")

And the development version from GitHub with:

BiocManager::install("mfansler/txcutr")

Conda/Mamba

Users managing R environments with Conda/Mamba can install the package with:

Conda

conda install -c conda-forge -c bioconda merv::r-txcutr

Mamba

mamba install -c conda-forge -c bioconda merv::r-txcutr

We strongly encourage users to create dedicated R environments. Do not install this in your base environment!

Example

A typical workflow for txcutr involves

• loading an existing annotation as TxDb object
• truncating the annotation
• exporting the truncated annotation (GTF)
• exporting supporting files (FASTA, merge TSV)

library(rtracklayer)
library(txcutr)
library(BSgenome.Hsapiens.UCSC.hg38)

## load human genome
hg38 <- BSgenome.Hsapiens.UCSC.hg38

## load human GENCODE annotation
txdb <- makeTxDbFromGFF("gencode.v38.annotaton.gtf.gz", organism="Homo sapiens")

## truncate to maximum of 500 nts
txdb_w500 <- truncateTxome(txdb, maxTxLength=500)

## export annotation
exportGTF(txdb_w500, file="gencode.v38.txcutr_w500.gtf.gz")

## export FASTA
exportFASTA(txdb_w500, genome=hg38, file="gencode.v38.txcutr_w500.fa.gz")

## export merge-table
exportMergeTable(txdb_w500, minDistance=200,
                 file="gencode.v38.txcutr_w500.merge.tsv.gz")

Citation

Below is the citation output from using citation('txcutr') in R. Please run this yourself to check for any updates on how to cite txcutr.

print(citation('txcutr'), bibtex = TRUE)
#> 
#> To cite package 'txcutr' in publications use:
#> 
#>   Mervin Fansler (2021). txcutr: Transcriptome CUTteR. R package
#>   version 0.99.1.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {txcutr: Transcriptome CUTteR},
#>     author = {Mervin Fansler},
#>     year = {2021},
#>     note = {R package version 0.99.1},
#>   }

Please note that the txcutr was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the txcutr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.