stjude/ChIPseqSpikeInFree: A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications

The detection of global histone modification changes can be addressed using exogenous reference Spike-in controls. However, many ChIP-seq data sets available in public depositories nowadays were done without including Spike-in procedure. In order to do quantitative comparisons between these data, researchers have to regenerate whole data set using spike-in ChIP-seq protocols – this is an infeasible solution sometime. A basic scaling factor calculation for these scenarios remains a challenge. We present ChIPseqSpikeInFree , a novel ChIP-seq normalization method to effectively determine scaling factors for samples across different conditions or treatments, which doesn't rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. It can reveal similar magnitude of global changes compared to spike-In method.

install.packages("remotes")
remotes::install_github("stjude/ChIPseqSpikeInFree")