tximeta

DOI: 10.18129/B9.bioc.tximeta  

Transcript Quantification Import with Automatic Metadata

Bioconductor version: Release (3.16)

Transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

Author: Michael Love [aut, cre], Charlotte Soneson [aut, ctb], Peter Hickey [aut, ctb], Rob Patro [aut, ctb], NIH NHGRI [fnd], CZI [fnd]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tximeta")

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("tximeta")

 

HTML R Script Transcript quantification import with automatic metadata
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics
Version 1.16.1
In Bioconductor since BioC 3.8 (R-3.5) (4.5 years)
License GPL-2
Depends
Imports SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix
LinkingTo
Suggests knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools
SystemRequirements
Enhances
URL https://github.com/mikelove/tximeta
Depends On Me rnaseqGene
Imports Me IsoformSwitchAnalyzeR
Suggests Me DESeq2, fishpond, fluentGenomics
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tximeta_1.16.1.tar.gz
Windows Binary tximeta_1.16.1.zip
macOS Binary (x86_64) tximeta_1.16.1.tgz
macOS Binary (arm64) tximeta_1.16.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/tximeta
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tximeta
Bioc Package Browser https://code.bioconductor.org/browse/tximeta/
Package Short Url https://bioconductor.org/packages/tximeta/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: