DESCRIPTION

Package: ChIPseqSpikeInFree
Title: A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
Version: 1.2.6
Date: 2020-08-31
Authors@R: 
    person(given = "Hongjian",
           family = "Jin",
           role = c("aut", "cre"),
           email = "hongjian.jin@stjude.org")
Description: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.
Depends:
  GenomicAlignments,
  GenomicRanges,  
  IRanges,
  R (>= 3.5.0),
  Rsamtools
License: GPL-3
Suggests:
  testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.1.1
Config/testthat/edition: 3