DOI: 10.18129/B9.bioc.tximport  

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

Import and summarize transcript-level estimates for transcript- and gene-level analysis

Bioconductor version: 3.16

Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

Author: Michael Love [cre,aut], Charlotte Soneson [aut], Mark Robinson [aut], Rob Patro [ctb], Andrew Parker Morgan [ctb], Ryan C. Thompson [ctb], Matt Shirley [ctb], Avi Srivastava [ctb]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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


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HTML R Script Importing transcript abundance datasets with tximport
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biocViews DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version 1.26.1
In Bioconductor since BioC 3.3 (R-3.3) (7 years)
License LGPL (>=2)
Imports utils, stats, methods
Suggests knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2(>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds
URL https://github.com/mikelove/tximport
Depends On Me
Imports Me alevinQC, BgeeCall, EventPointer, IsoformSwitchAnalyzeR, singleCellTK, tximeta
Suggests Me BANDITS, DESeq2, HumanTranscriptomeCompendium, SummarizedBenchmark, variancePartition
Links To Me
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Source Package tximport_1.26.1.tar.gz
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macOS Binary (arm64) tximport_1.26.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/tximport
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tximport
Bioc Package Browser https://code.bioconductor.org/browse/tximport/
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