tximport
Transcript quantification import for modular pipelines
Science Score: 49.0%
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Keywords
bioconductor
deseq2
rnaseq
Keywords from Contributors
bioconductor-package
bioinformatics
core-package
derfinder
rhdf5
hdf5
mirror
pathway-analysis
image-analysis
bioc
Last synced: 6 months ago
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Repository
Transcript quantification import for modular pipelines
Statistics
- Stars: 141
- Watchers: 14
- Forks: 34
- Open Issues: 1
- Releases: 0
Topics
bioconductor
deseq2
rnaseq
Created over 10 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Code of conduct
README.md
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Description of methods and analysis described in:
- Charlotte Soneson, Michael I. Love, Mark D. Robinson. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences, F1000Research, 4:1521, December 2015. doi: 10.12688/f1000research.7563.1
Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream statistical analysis packages such as edgeR, DESeq2, limma-voom. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.
See examples in the vignette.
Notes:
- tximport as of version 1.3.9 will import inferential replicates (Gibbs samples or bootstrap samples) from Salmon, Sailfish or kallisto.
- Though we provide here functionality for performing gene-level
differential expression using summarized transcript-level estimates,
this is does not mean we suggest that users only perform gene-level
analysis. Gene-level differential expression can be complemented
with transcript- or exon-level analysis. The argument
txOut=TRUEcan be used to generate transcript-level matrices.
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: 3
- Watch event: 5
- Issue comment event: 5
- Push event: 2
- Fork event: 1
Last Year
- Issues event: 3
- Watch event: 5
- Issue comment event: 5
- Push event: 2
- Fork event: 1
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| mikelove | m****e@g****m | 203 |
| Nitesh Turaga | n****a@g****m | 14 |
| Mike Love | m****e | 11 |
| Dan Tenenbaum | d****a@f****g | 4 |
| Herve Pages | h****s@f****g | 4 |
| J Wokaty | j****y@s****u | 4 |
| Rob Patro | r****o@g****m | 4 |
| mikelove | m****1@g****m | 3 |
| Alexander Toenges | 2****t | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| Rob Patro | r****p | 2 |
| J Wokaty | j****y | 2 |
| LTLA | i****s@g****m | 1 |
| Martin Morgan | m****n@f****g | 1 |
| roryk | r****r@g****m | 1 |
| Matt Shirley | m****5@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 50
- Total pull requests: 9
- Average time to close issues: about 1 month
- Average time to close pull requests: about 2 months
- Total issue authors: 33
- Total pull request authors: 6
- Average comments per issue: 2.44
- Average comments per pull request: 2.22
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: about 1 hour
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mikelove (9)
- csoneson (3)
- stephenturner (3)
- marwa38 (2)
- mdshw5 (2)
- FlorianRocher (2)
- koenvandenberge (2)
- PeteHaitch (2)
- edoardobertolini (1)
- Ci-TJ (1)
- kokitsuyuzaki (1)
- BitaoQiu (1)
- cindywen96 (1)
- SylwiaPiatkowska (1)
- AhmedSAHassan (1)
Pull Request Authors
- ATpoint (3)
- rob-p (2)
- andrewparkermorgan (1)
- LTLA (1)
- roryk (1)
- mdshw5 (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 442,484 total
- Total dependent packages: 13
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
- Homepage: https://github.com/thelovelab/tximport
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.pdf
- License: LGPL (>=2)
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Latest release: 1.36.1
published 8 months ago
Rankings
Dependent repos count: 0.0%
Stargazers count: 1.3%
Forks count: 1.3%
Average: 2.3%
Dependent packages count: 4.1%
Downloads: 5.1%
Maintainers (1)
Last synced:
6 months ago
Dependencies
DESCRIPTION
cran
- methods * imports
- stats * imports
- utils * imports
- DESeq2 >= 1.11.6 suggests
- Matrix * suggests
- TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
- edgeR * suggests
- eds * suggests
- jsonlite * suggests
- knitr * suggests
- limma * suggests
- matrixStats * suggests
- readr >= 0.2.2 suggests
- rhdf5 * suggests
- rmarkdown * suggests
- testthat * suggests
- tximportData * suggests