Name Mode Size
.github 040000
R 040000
inst 040000
man 040000
pkgdown 040000
tests 040000
vignettes 040000
.gitignore 100644 0 kb 100644 3 kb
DESCRIPTION 100644 1 kb
NAMESPACE 100644 3 kb 100644 7 kb 100644 3 kb
# tximeta <img id="tximeta_logo" src="man/figures/tximeta.png" align="right" width="125"/> [![R build status](]( # Automatic metadata for RNA-seq *tximeta* provides a set of functions for conveniently working with metadata for transcript quantification data in Bioconductor. The `tximeta()` function imports quantification data from *Salmon* or other quantifiers, and returns a [SummarizedExperiment]( object. *tximeta* works natively with [Salmon](, [alevin](, or [piscem-infer](, but can easily be configured to work with any transcript quantification tool. If `tximeta()` recognizes the reference transcripts used for quantification, it will automatically download relevant information about the location of the transcripts in the correct genome. *These actions happen in the background without requiring any extra effort or information from the user.* This metadata is attached to the *SummarizedExperiment* in the `metadata()` and `rowRanges()` slots. For a list of the reference transcriptomes supported by `tximeta()`, see the "Pre-computed digests" section of the vignette in the `Get started` tab. We call the computed identifier for the reference transcriptome a "digest" or sometimes a "checksum". Further steps are also facilitated, e.g. `summarizeToGene()`, `addIds()`, or even `retrieveCDNA()` (the transcripts used for quantification) or `retrieveDb()` (the correct *TxDb* or *EnsDb* to match the quantification data). # How it works The key idea behind *tximeta* is that *Salmon*, *alevin*, and *piscem-infer* propagate a hash value summarizing the reference transcripts into each quantification directory it outputs. *tximeta* can be used with other tools as long as the [hash of the transcripts]( is also included in the output directories. See `customMetaInfo` argument of `tximeta()` for more details. ![](man/figures/diagram.png) # Reference A reference for *tximeta* 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 provenance > identification in RNA-seq" *PLOS Computational Biology* (2020) > [doi: 10.1371/journal.pcbi.1007664]( # Feedback We would love to hear your feedback. Please post to [Bioconductor support site]( for software usage help or post an [Issue on GitHub](, for software development questions. # Funding tximeta was developed as part of NIH NHGRI R01-HG009937. tximeta was also supported by the Chan Zuckerberg Initiative as part of the EOSS grants. ![](man/figures/czi.png)