https://github.com/bioconductor-source/spiky
Science Score: 23.0%
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
-
✓Academic publication links
Links to: sciencedirect.com -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 18.9 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
spiky
Spike-ins for everyone
Analysis of cfMeDIP-seq data with spike-in control sequences. For more information, see Wilson, et. al, Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls, Cell Reports Methods, 2022. (https://www.sciencedirect.com/science/article/pii/S266723752200176X?via%3Dihub)
Please note that spiky strongly suggests a recent version of R (4.0 or newer; 3.6 or newer is required).
This restriction may be removed if our dependencies can tolerate it.
Installing
To install this package, start R (version "3.6" or later) and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("trichelab/spiky")
For developers
The repository includes a Makefile to facilitate some common tasks.
Running tests
$ make test. Requires the testthat package. You can also specify a specific test file or files to run by adding a "file=" argument, like $ make test file=logging. test_package will do a regular-expression pattern match within the file names. See its documentation in the testthat package.
Updating documentation
$ make doc. Requires the roxygen2 package.
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
- GenomicRanges * depends
- R >= 3.6.0 depends
- Rsamtools * depends
- BSgenome * imports
- Biostrings * imports
- BlandAltmanLeh * imports
- GenomeInfoDb * imports
- GenomicAlignments * imports
- IRanges * imports
- S4Vectors * imports
- bamlss * imports
- ggplot2 * imports
- graphics * imports
- methods * imports
- scales * imports
- stats * imports
- tools * imports
- utils * imports
- BSgenome.Hsapiens.UCSC.hg38.masked * suggests
- BSgenome.Mmusculus.UCSC.mm10.masked * suggests
- BiocManager * suggests
- covr * suggests
- devtools * suggests
- knitr * suggests
- markdown * suggests
- rmarkdown * suggests
- testthat * suggests