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Bioconductor - tximeta (development version)

tximeta

This is the development version of tximeta; for the stable release version, see tximeta.

Transcript Quantification Import with Automatic Metadata

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics Version 1.27.2 In Bioconductor since BioC 3.8 (R-3.5) (6.5 years) License GPL-2 Depends R (>= 4.1.0) Imports SummarizedExperiment(>= 1.39.1), tximport, jsonlite, S4Vectors, IRanges, GenomicRanges(>= 1.61.1), AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, Seqinfo, tools, utils, methods, Matrix System Requirements URL https://github.com/thelovelab/tximeta See More 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.

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