tximeta

Transcript Quantification Import with Automatic Metadata

Bioconductor version: Release (3.20)

Transcript quantification import from Salmon and other quantifiers 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 "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics
Version	1.24.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 years)
License	GPL-2
Depends
Imports	SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix
System Requirements
URL	https://github.com/thelovelab/tximeta

Suggests	knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools
Linking To
Enhances
Depends On Me	rnaseqGene
Imports Me	IsoformSwitchAnalyzeR
Suggests Me	DESeq2, fishpond, fluentGenomics
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	tximeta_1.24.0.tar.gz
Windows Binary (x86_64)	tximeta_1.24.0.zip
macOS Binary (x86_64)	tximeta_1.24.0.tgz
macOS Binary (arm64)	tximeta_1.24.0.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