Transcript Quantification Import with Automatic Metadata

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Documentation for package ‘tximeta’ version 1.27.12

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

tximeta-package	Import transcript quantification with metadata
addCDS	Add CDS to rowRanges of a transcript-level SummarizedExperiment
addExons	Add exons to rowRanges of a transcript-level SummarizedExperiment
addIds	Add IDs to rowRanges of a SummarizedExperiment
getTximetaBFC	Get or set the directory of the BiocFileCache used by tximeta
importData	Import quantification across mixed reference transcripts
inspectDigests	Inspect digest matches from 'importData()' imported data
linkedTxome	Make and load linked transcriptomes (linked GTF and FASTA)
linkedTxpData	Make linked transcript data (linked GRanges)
loadLinkedTxome	Make and load linked transcriptomes (linked GTF and FASTA)
makeDGEList	Make a DGEList from tximeta output
makeLinkedTxome	Make and load linked transcriptomes (linked GTF and FASTA)
makeLinkedTxpData	Make linked transcript data (linked GRanges)
retrieveCDNA	Retrieve the cDNA transcript sequence for a SummarizedExperiment
retrieveDb	Retrieve the TxDb or EnsDb associated with a SummarizedExperiment
setTximetaBFC	Get or set the directory of the BiocFileCache used by tximeta
splitSE	Split SummarizedExperiment by gene categories
summarizeToGene-method	Summarize estimated quantitites to gene-level
tximeta	Import transcript quantification with metadata
updateMetadata	Update transcript metadatda for 'importData()' imported data