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AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification

2019 Nucleic Acids Research  
We applied AIControl to 410 IP datasets in the ENCODE ChIP-seq database, using 440 control datasets from 107 cell types to impute background signal.  ...  available control ChIP-seq datasets.  ...  ACKNOWLEDGEMENTS We would like to acknowledge the following people for testing the AIControl software and giving suggestions on improving its usability: Ayse Berceste Dincer, Joseph D.  ... 
doi:10.1093/nar/gkz156 pmid:30869146 pmcid:PMC6547432 fatcat:2zkyqld7dvhi7kvoeahta26dei

AIControl: Replacing matched control experiments with machine learning improves ChIP-seq peak identification [article]

Naozumi Hiranuma, Scott M Lundberg, Su-In Lee
2018 bioRxiv   pre-print
AIControl used 455 control ChIP-seq datasets from 107 cell lines and 9 laboratories to impute background ChIP-seq noise signals.  ...  Because ChIP-seq is highly susceptible to background noise, the current practice obtains one matched "control" ChIP-seq dataset and estimates position-wise background distributions using ChIP-seq signals  ...  experiments. 558 AIControl better removes common background signal among datasets.  ... 
doi:10.1101/278762 fatcat:i6s3krrvyfdh3li5r5s6s7k6gq