[](https://github.com/trichelab/spiky) # spiky [](https://travis-ci.org/trichelab/spiky) [](https://codecov.io/gh/trichelab/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](https://github.com/hadley/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](https://github.com/klutometis/roxygen) package.