tximeta

DOI: 10.18129/B9.bioc.tximeta    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see tximeta.

Transcript Quantification Import with Automatic Metadata

Bioconductor version: 3.10

Transcript quantification import from Salmon with automatic population of metadata and transcript ranges. Filtered, combined, or de novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for reproducible analyses.

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

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version	1.4.5
In Bioconductor since	BioC 3.8 (R-3.5) (1.5 years)
License	GPL-2
Depends
Imports	SummarizedExperiment, tximport, jsonlite, S4Vectors, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, Biostrings, BiocFileCache, tibble, GenomeInfoDb, rappdirs, utils, methods
LinkingTo
Suggests	knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, limma, devtools
SystemRequirements
Enhances
URL	https://github.com/mikelove/tximeta
Depends On Me	rnaseqGene
Imports Me
Suggests Me	DESeq2, fishpond
Links To Me
Build Report

Package Archives

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

Source Package	tximeta_1.4.5.tar.gz
Windows Binary	tximeta_1.4.5.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	tximeta_1.4.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tximeta
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tximeta
Package Short Url	https://bioconductor.org/packages/tximeta/
Package Downloads Report	Download Stats