tximeta-package: Import transcript quantification with metadata

In mikelove/tximeta: Transcript Quantification Import with Automatic Metadata

Import transcript quantification with metadata

Description

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.

Details

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:

https://github.com/thelovelab/tximeta

Author(s)

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

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 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

mikelove/tximeta documentation built on Feb. 26, 2024, 4:32 a.m.