tximeta
Transcript quantification import with automatic metadata detection
Science Score: 49.0%
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Repository
Transcript quantification import with automatic metadata detection
Basic Info
- Host: GitHub
- Owner: thelovelab
- Language: R
- Default Branch: devel
- Homepage: https://thelovelab.github.io/tximeta/
- Size: 2 MB
Statistics
- Stars: 67
- Watchers: 12
- Forks: 11
- Open Issues: 10
- Releases: 0
Metadata Files
README.md
tximeta 
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.
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.
Owner
- Name: The Love Lab
- Login: thelovelab
- Kind: organization
- Email: michaelisaiahlove [at] gmail
- Location: United States of America
- Website: https://mikelove.github.io
- Twitter: mikelove
- Repositories: 1
- Profile: https://github.com/thelovelab
Software produced by members of the Love Lab (UNC-Chapel Hill)
GitHub Events
Total
- Issues event: 9
- Watch event: 1
- Issue comment event: 13
- Push event: 20
- Create event: 1
Last Year
- Issues event: 9
- Watch event: 1
- Issue comment event: 13
- Push event: 20
- Create event: 1
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Last synced: over 2 years ago
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Last synced: 6 months ago
All Time
- Total issues: 80
- Total pull requests: 7
- Average time to close issues: 4 months
- Average time to close pull requests: about 3 hours
- Total issue authors: 49
- Total pull request authors: 1
- Average comments per issue: 4.24
- Average comments per pull request: 1.71
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 0
- Average time to close issues: 2 months
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- Average comments per issue: 1.4
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mikelove (23)
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- Knievl (1)
Pull Request Authors
- csoneson (7)
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 132,107 total
- Total dependent packages: 3
- Total dependent repositories: 0
- Total versions: 10
- Total maintainers: 1
bioconductor.org: tximeta
Transcript Quantification Import with Automatic Metadata
- Homepage: https://github.com/thelovelab/tximeta
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.pdf
- License: GPL-2
-
Latest release: 1.26.1
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- AnnotationDbi * imports
- AnnotationHub * imports
- BiocFileCache * imports
- Biostrings * imports
- GenomeInfoDb * imports
- GenomicFeatures * imports
- GenomicRanges * imports
- IRanges * imports
- Matrix * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- ensembldb * imports
- jsonlite * imports
- methods * imports
- tibble * imports
- tools * imports
- tximport * imports
- utils * imports
- DESeq2 * suggests
- devtools * suggests
- edgeR * suggests
- fishpond * suggests
- knitr * suggests
- limma * suggests
- org.Dm.eg.db * suggests
- rmarkdown * suggests
- testthat * suggests
- tximportData * suggests