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>

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

Installation

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

Details

biocViews Annotation, DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version 1.4.5
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Depends
Imports SummarizedExperiment, tximport, jsonlite, S4Vectors, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, Biostrings, BiocFileCache, tibble, GenomeInfoDb, rappdirs, utils, methods
System Requirements
URL https://github.com/mikelove/tximeta
See More
Suggests knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, limma, devtools
Linking To
Enhances
Depends On Me rnaseqGene
Imports Me
Suggests Me DESeq2, fishpond
Links To Me
Build Report 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
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 3.10 Source Archive