This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see tximeta.
Bioconductor version: 3.8
Transcript quantification import from Salmon with automatic population of metadata and transcript ranges. Filtered, combined, or de novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for reproducible analyses.
Author: Michael Love [aut, cre], Rob Patro [aut, ctb], Peter Hickey [aut, ctb], Charlotte Soneson [aut, ctb]
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
Citation (from within R,
enter citation("tximeta")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("tximeta")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tximeta")
HTML | R Script | Transcript quantification import with automatic metadata |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics |
Version | 1.0.3 |
In Bioconductor since | BioC 3.8 (R-3.5) (0.5 years) |
License | GPL-2 |
Depends | |
Imports | SummarizedExperiment, tximport, jsonlite, S4Vectors, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, tibble, GenomeInfoDb, rappdirs, utils, methods |
LinkingTo | |
Suggests | knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, devtools |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | scater |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | tximeta_1.0.3.tar.gz |
Windows Binary | tximeta_1.0.3.zip |
Mac OS X 10.11 (El Capitan) | tximeta_1.0.3.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/tximeta |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tximeta |
Package Short Url | http://bioconductor.org/packages/tximeta/ |
Package Downloads Report | Download Stats |
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