DOI: 10.18129/B9.bioc.tximeta  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see tximeta.

Transcript Quantification Import with Automatic Metadata

Bioconductor version: 3.16

Transcript quantification import from Salmon and alevin 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")):


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biocViews Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics
Version 1.16.1
In Bioconductor since BioC 3.8 (R-3.5) (4.5 years)
License GPL-2
Imports SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix
Suggests knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools
URL https://github.com/mikelove/tximeta
Depends On Me rnaseqGene
Imports Me IsoformSwitchAnalyzeR
Suggests Me DESeq2, fishpond, fluentGenomics
Links To Me
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Source Package tximeta_1.16.1.tar.gz
Windows Binary tximeta_1.16.1.zip
macOS Binary (x86_64) tximeta_1.16.1.tgz
macOS Binary (arm64) tximeta_1.16.1.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/
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