# Transcript Quantification Import with Automatic Metadata

## Documentation for package ‘tximeta’ version 1.31.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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