tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Bioconductor version: 3.24 · Package version: 1.41.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tximport")Details
| Maintainer | Michael Love <michaelisaiahlove@gmail.com> |
| 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] |
| License | LGPL (>=2) |
| URL | https://github.com/thelovelab/tximport |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/tximport/ |
Citation
From within R, enter citation("tximport"):
Michael Love, Charlotte Soneson, Mark Robinson. tximport: Import and summarize transcript-level estimates for transcript- and gene-level analysis. doi:10.18129/B9.bioc.tximport, R package version 1.41.0, https://bioconductor.org/packages/tximport.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | tximport_1.41.0.tar.gz |
| Windows binary (x86_64) | tximport_1.41.0.zip |
| macOS binary (arm64) | tximport_1.41.0.tgz |
| macOS binary (x86_64) | tximport_1.41.0.tgz |
Dependencies
Imports: utils, stats, methods
Suggests: knitr, rmarkdown, testthat, tximportData (>= 1.41.1), TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR (>= 4.9.2), DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds
Reverse dependencies
Imports Me (12): alevinQC, BgeeCall, CleanUpRNAseq, cpam, DifferentialRegulation, EventPointer, ExpHunterSuite, EZbakR, IsoformSwitchAnalyzeR, singleCellTK, TDbasedUFE, tximeta
Suggests Me (3): BANDITS, DESeq2, variancePartition