tximeta
Transcript Quantification Import with Automatic Metadata
Bioconductor version: 3.23 · Package version: 1.30.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tximeta")Details
| Maintainer | Michael Love <michaelisaiahlove@gmail.com> |
| Author | Michael Love [aut, cre], Charlotte Soneson [aut, ctb], Peter Hickey [aut, ctb], Rob Patro [aut, ctb], NIH NHGRI [fnd], CZI [fnd] |
| License | GPL-2 |
| URL | https://github.com/thelovelab/tximeta |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, LongRead, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/tximeta/ |
Citation
From within R, enter citation("tximeta"):
Michael Love, Charlotte Soneson, Peter Hickey, Rob Patro. tximeta: Transcript Quantification Import with Automatic Metadata. doi:10.18129/B9.bioc.tximeta, R package version 1.30.0, https://bioconductor.org/packages/tximeta.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | tximeta_1.30.0.tar.gz |
| Windows binary (x86_64) | tximeta_1.30.0.zip |
| macOS binary (arm64) | tximeta_1.30.0.tgz |
| macOS binary (x86_64) | tximeta_1.30.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: SummarizedExperiment (>= 1.39.1), tximport, jsonlite, S4Vectors, IRanges, GenomicRanges (>= 1.61.1), AnnotationDbi, DBI, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, Seqinfo, tools, utils, methods, Matrix
Suggests: knitr, rmarkdown, testthat, tximportData (>= 1.37.5), org.Dm.eg.db, DESeq2, edgeR (>= 4.9.2), limma, devtools, macrophage
Reverse dependencies
Depends On Me (1): rnaseqGene
Imports Me (1): IsoformSwitchAnalyzeR
Suggests Me (3): DESeq2, fishpond, fluentGenomics