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tximeta provides a set of functions for conveniently working withmetadata for transcript quantification data in Bioconductor. Thetximeta() function imports quantification data fromSalmon orother quantifiers, and returns aSummarizedExperimentobject.tximeta works natively withSalmon,alevin,orpiscem-infer,but can easily be configured to work with any transcriptquantification tool.

Iftximeta() recognizes the reference transcripts usedfor quantification, it will automatically download relevantinformation about the location of the transcripts in the correct genome.These actions happen in the background without requiring any extraeffort or information from the user.

This metadata is attached to theSummarizedExperiment in themetadata() androwRanges() slots.

For a list of the reference transcriptomes supported bytximeta(),see the "Pre-computed digests" section of the vignette in theGet started tab. We call the computed identifier for the referencetranscriptome a "digest" or sometimes a "checksum".

Further steps are also facilitated, e.g.summarizeToGene(),addIds(),or evenretrieveCDNA() (the transcripts used for quantification) orretrieveDb() (the correctTxDb orEnsDb to match thequantification data).

The key idea behindtximeta is thatSalmon,alevin, andpiscem-infer propagate a hash valuesummarizing the reference transcripts into each quantificationdirectory it outputs.tximeta can be used with other tools as longas thehash of the transcriptsis also included in the output directories. SeecustomMetaInfoargument oftximeta() for more details.

A reference fortximeta package is:

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

We would love to hear your feedback. Please post toBioconductor support site forsoftware usage help or post anIssue on GitHub,for software development questions.

tximeta was developed as part of NIH NHGRI R01-HG009937.

tximeta was also supported by the Chan Zuckerberg Initiative as partof the EOSS grants.