tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Bioconductor version: Release (3.19)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.32.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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, DESeq2(>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | BgeeCall, DifferentialRegulation, EventPointer, IsoformSwitchAnalyzeR, TDbasedUFE, alevinQC, singleCellTK, tximeta, ExpHunterSuite, seeker |
| Suggests Me | BANDITS, DESeq2, HumanTranscriptomeCompendium, variancePartition |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tximport_1.32.0.tar.gz |
| Windows Binary (x86_64) | tximport_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | tximport_1.32.0.tgz |
| macOS Binary (arm64) | tximport_1.32.0.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 |