https://github.com/bioconductor-source/tradeseq
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: other
- Language: R
- Default Branch: devel
- Size: 54.5 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
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: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
Total
Last Year
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc v2-branch composite
- r-lib/actions/setup-r v2-branch composite
- 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
- DelayedMatrixStats * suggests
- clusterExperiment * suggests
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests