The tximeta package imports abundances (TPM), estimated counts,
and effective lengths from Salmon, alevin, piscem or other quantification
tools, and will output a SummarizedExperiment object. For
Salmon / alevin / piscem quantification data, 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,SummarizedExperiment-method - summarize quants to gene-level
retrieveDb - retrieve the transcript database
addIds - add transcript or gene ID (see gene argument)
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:
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
Useful links: