tximeta-package: Import transcript-level quantification data with automatic...
In tximeta: Transcript Quantification Import with Automatic Metadata

Description Details Author(s) References

The tximeta package imports abundances (TPM), estimated counts, and effective lengths from Salmon, alevin, or other quantification tools, and will output a SummarizedExperiment object. For Salmon and alevin quantification directories, tximeta will try 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.

The main functions are:

tximeta - with key argument: coldata
summarizeToGene - summarize quants to gene-level
retrieveDb - retrieve the transcript database
addIds - add transcript or gene ID (see gene argument)
addExons - convert from GRanges to GRangesList

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/mikelove/tximeta

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

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 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

tximeta documentation built on April 13, 2021, 6:01 p.m.