Import transcript quantification with metadata

The tximeta package imports abundances (TPM), estimated counts, and effective lengths from quantification tools, and will output a SummarizedExperiment (SE) object. For salmon and related quantification tools, tximeta() will attempt to identify the correct provenance of the reference transcripts and automatically attach the transcript ranges to the SummarizedExperiment, to facilitate downstream integration with other datasets. The automatic identification of reference transcripts should work out-of-the-box for human or mouse transcriptomes from the sources: GENCODE, Ensembl, or RefSeq. See also importData() for importing data when the reference transcripts were derived from a mix of annotated (e.g. GENCODE) and novel or custom transcripts.

Details

The main functions are:

tximeta() - with key argument coldata specifying sample information
summarizeToGene() - summarize quantification to gene-level
importData() - import quantification with mixed reference transcript sets

All software-related questions should be posted to the Bioconductor Support Site:

https://support.bioconductor.org

The code can be viewed at the GitHub repository, which also lists the contributor code of conduct:

https://github.com/thelovelab/tximeta

References

tximeta reference:

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson N. Tessa Pierce, Lori Shepherd, Martin Morgan, Rob Patro (2020) Tximeta: reference sequence checksums for provenance identification in RNA-seq. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1007664

tximport reference (the effective length GLM offset and counts-from-abundance):

Charlotte Soneson, Michael I. Love, Mark D. Robinson (2015) Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research. http://doi.org/10.12688/f1000research.7563

Author

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