tximport
This is the development version of tximport; for the stable release version, see tximport.
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Bioconductor version: Development (3.24)
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("tximport")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("tximport")
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("tximport")| Importing transcript abundance datasets with tximport | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | LGPL (>=2) |
| Depends | |
| Imports | utils, stats, methods |
| System Requirements | |
| URL | https://github.com/thelovelab/tximport |
See More
| Suggests | knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR(>= 4.9.2), DESeq2(>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | alevinQC, BgeeCall, CleanUpRNAseq, DifferentialRegulation, EventPointer, IsoformSwitchAnalyzeR, singleCellTK, TDbasedUFE, tximeta, ExpHunterSuite, cpam, EZbakR |
| Suggests Me | BANDITS, DESeq2, variancePartition |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (big-sur-x86_64) | tximport_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | tximport_1.41.0.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/ |
| Package Short Url | https://bioconductor.org/packages/tximport/ |
| Package Downloads Report | Download Stats |