Name Mode Size
R 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
DESCRIPTION 100644 1 kb
NAMESPACE 100644 2 kb 100644 2 kb
README.Rmd 100644 5 kb 100644 5 kb
<!-- is generated from README.Rmd. Please edit that file --> # txcutr <!-- badges: start --> [![R build status](]( [![codecov](]( [![Anaconda-Server Badge](]( [![Anaconda-Server Badge](]( <!-- badges: end --> ## 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: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("txcutr") ``` And the development version from [GitHub]( with: ``` r BiocManager::install("mfansler/txcutr") ``` ### Conda/Mamba Users managing R environments with Conda/Mamba can install the package with: **Conda** ``` bash conda install -c conda-forge -c bioconda merv::r-txcutr ``` **Mamba** ``` bash 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) ``` r 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**. ``` r 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](*.