tradeSeq
TRAjectory-based Differential Expression analysis for SEQuencing data
Science Score: 59.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
2 of 11 committers (18.2%) from academic institutions -
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Keywords from Contributors
Repository
TRAjectory-based Differential Expression analysis for SEQuencing data
Basic Info
Statistics
- Stars: 279
- Watchers: 6
- Forks: 32
- Open Issues: 36
- Releases: 1
Metadata Files
README.md
R package: tradeSeq
<!-- badges: start -->
TRAjectory Differential Expression analysis for SEQuencing data
tradeSeq provides a flexible method for discovering genes that are differentially expressed along one or multiple lineages, using a variety of tests suited to answer many questions of interest.
Installation
To install the current version of tradeSeq in Bioconductor, run.
if(!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("tradeSeq")
To install the development version in R, run
r
devtools::install_github("statOmics/tradeSeq")
The installation should only take a few seconds. The dependencies of the package are listed in the DESCRIPTION file of the package.
Changes
Major changes are reported in the NEWS file, make sure to check it out if you want to follow the latest developments.
Issues and bug reports
Please use https://github.com/statOmics/tradeSeq/issues to submit issues, bug reports, and comments.
Usage
Start with the vignette online.
Cheatsheet
You can also refer to this cheatsheet to undersand a common workflow
Contributing and requesting
A number of tests have been implemented in tradeSeq, but researchers may be interested in other hypotheses that current implementations may not be able to address. We therefore welcome contributions on GitHub on novel tests based on the tradeSeq model. Similar, you may also request novel tests to be implemented in tradeSeq by the developers, preferably by adding an issue on the GitHub repository. If we feel that the suggested test is widely applicable, we will implement it in tradeSeq.
Owner
- Name: statOmics
- Login: statOmics
- Kind: organization
- Website: https://statomics.github.io
- Repositories: 33
- Profile: https://github.com/statOmics
GitHub Events
Total
- Issues event: 7
- Watch event: 32
- Issue comment event: 13
- Push event: 9
- Pull request event: 1
- Fork event: 5
Last Year
- Issues event: 7
- Watch event: 32
- Issue comment event: 13
- Push event: 9
- Pull request event: 1
- Fork event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Hector | h****x@b****u | 239 |
| koenvandenberge | k****e@u****e | 222 |
| koenvandenberge | k****e@g****m | 172 |
| Koen Van den Berge | K****4@i****m | 14 |
| Nitesh Turaga | n****a@g****m | 12 |
| Kelly Street | k****t@r****l | 5 |
| Koen Van den Berge | k****e@w****e | 4 |
| statOmics | l****t@u****e | 3 |
| J Wokaty | j****y@s****u | 2 |
| szcf-weiya | s****a@g****m | 1 |
| Angela Ling | a****a@A****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 97
- Total pull requests: 4
- Average time to close issues: 3 months
- Average time to close pull requests: about 1 month
- Total issue authors: 74
- Total pull request authors: 3
- Average comments per issue: 2.71
- Average comments per pull request: 0.5
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 7
- Pull requests: 2
- Average time to close issues: 5 months
- Average time to close pull requests: 3 months
- Issue authors: 7
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.5
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- pchiang5 (5)
- FADHLyemen (4)
- Sophia409 (3)
- beazors (3)
- nickhir (3)
- lihong911002 (2)
- flde (2)
- AndreaYCT (2)
- JesseRop (2)
- Dazcam (2)
- fluentin44 (2)
- carbycrab (2)
- gabrielnegreira (2)
- yashuap (2)
- 83years (1)
Pull Request Authors
- Alexis-Varin (2)
- szcf-weiya (1)
- carbycrab (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 46,588 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: tradeSeq
trajectory-based differential expression analysis for sequencing data
- Homepage: https://statomics.github.io/tradeSeq/index.html
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/tradeSeq/inst/doc/tradeSeq.pdf
- License: MIT + file LICENSE
-
Latest release: 1.22.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6 depends
- Biobase * imports
- BiocParallel * imports
- MASS * imports
- Matrix * imports
- RColorBrewer * imports
- S4Vectors * imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- TrajectoryUtils * imports
- edgeR * imports
- ggplot2 * imports
- igraph * imports
- magrittr * imports
- matrixStats * imports
- methods * imports
- mgcv * imports
- pbapply * imports
- princurve * imports
- slingshot * imports
- tibble * imports
- viridis * imports
- clusterExperiment * suggests
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc master composite
- r-lib/actions/setup-r master composite