tximeta

DOI: 10.18129/B9.bioc.tximeta    

Transcript Quantification Import with Automatic Metadata

Bioconductor version: Release (3.8)

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>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("tximeta", version = "3.8")

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, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version 1.0.1
License GPL-2
Depends
Imports SummarizedExperiment, tximport, jsonlite, S4Vectors, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, tibble, GenomeInfoDb, rappdirs, utils, methods
LinkingTo
Suggests knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, devtools
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me scater
Links To Me
Build Report  

Package Archives

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

Source Package tximeta_1.0.1.tar.gz
Windows Binary tximeta_1.0.1.zip
Mac OS X 10.11 (El Capitan) tximeta_1.0.1.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 http://bioconductor.org/packages/tximeta/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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