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.