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[![Spiky](vignettes/spiky-small.png)]( # spiky [![Build Status](]( [![codecov](]( # 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. ( 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.