Package: tximeta 1.25.0

Michael Love

tximeta: Transcript Quantification Import with Automatic Metadata

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.

Authors:Michael Love [aut, cre], Charlotte Soneson [aut, ctb], Peter Hickey [aut, ctb], Rob Patro [aut, ctb], NIH NHGRI [fnd], CZI [fnd]

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tximeta.pdf |tximeta.html✨
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NEWS

# Install 'tximeta' in R:

install.packages('tximeta', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thelovelab/tximeta/issues

On BioConductor:tximeta-1.25.0(bioc 3.21)tximeta-1.24.0(bioc 3.20)

annotation genomeannotation dataimport preprocessing rnaseq singlecell transcriptomics transcription geneexpression functionalgenomics reproducibleresearch reportwriting immunooncology

10.66 score 67 stars 1 packages 450 scripts 2.0k downloads 11 mentions 13 exports 101 dependencies

Last updated 23 days agofrom:eab5dbe3ed. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:addCDS addExons addIds getTximetaBFC loadLinkedTxome makeDGEList makeLinkedTxome retrieveCDNA retrieveDb setTximetaBFC splitSE summarizeToGene tximeta

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr ensembldb fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker tximport UCSC.utils utf8 vctrs withr XML xml2 XVector yaml zlibbioc

Tximeta: transcript quantification import with automatic metadata

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Rob Patro

Rendered fromtximeta.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-03-18
Started: 2018-07-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Import transcript quantification with metadata	tximeta-package
Add CDS to rowRanges of a transcript-level SummarizedExperiment	addCDS
Add exons to rowRanges of a transcript-level SummarizedExperiment	addExons
Add IDs to rowRanges of a SummarizedExperiment	addIds
Get or set the directory of the BiocFileCache used by tximeta	getTximetaBFC setTximetaBFC
Make and load linked transcriptomes ("linkedTxome")	linkedTxome loadLinkedTxome makeLinkedTxome
Make a DGEList from tximeta output	makeDGEList
Retrieve the cDNA transcript sequence for a SummarizedExperiment	retrieveCDNA
Retrieve the TxDb or EnsDb associated with a SummarizedExperiment	retrieveDb
Split SummarizedExperiment by gene categories	splitSE
Summarize estimated quantitites to gene-level	summarizeToGene,SummarizedExperiment-method
Import transcript quantification with metadata	tximeta