tximeta
Transcript Quantification Import with Automatic Metadata
Bioconductor version: Release (3.19)
Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.
Author: Michael Love [aut, cre], Charlotte Soneson [aut, ctb], Peter Hickey [aut, ctb], Rob Patro [aut, ctb], NIH NHGRI [fnd], CZI [fnd]
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("tximeta")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tximeta")
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("tximeta")| Transcript quantification import with automatic metadata | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics |
| Version | 1.22.1 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 years) |
| License | GPL-2 |
| Depends | |
| Imports | SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix |
| System Requirements | |
| URL | https://github.com/thelovelab/tximeta |
See More
| Suggests | knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools |
| Linking To | |
| Enhances | |
| Depends On Me | rnaseqGene |
| Imports Me | IsoformSwitchAnalyzeR |
| Suggests Me | DESeq2, fishpond, fluentGenomics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tximeta_1.22.1.tar.gz |
| Windows Binary (x86_64) | tximeta_1.22.1.zip |
| macOS Binary (x86_64) | tximeta_1.22.1.tgz |
| macOS Binary (arm64) | tximeta_1.22.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tximeta |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tximeta |
| Bioc Package Browser | https://code.bioconductor.org/browse/tximeta/ |
| Package Short Url | https://bioconductor.org/packages/tximeta/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |