DoubleChEC program to identify transcription factor binding sites from mapped ChEC-seq data

ChIP-seq (chromatin immunoprecipitation followed by sequencing) is
commonly used to identify genome-wide protein-DNA interactions. However,
ChIP-seq often gives a low yield, which is not ideal for quantitative
outcomes. An alternative method to ChIP-seq is ChEC-seq (Chromatin
endogenous cleavage with high-throughput sequencing). In this method, the
endogenous TF (transcription factor) of interest is fused with MNase
(micrococcal nuclease) that non-specifically cleaves DNA near binding
sites. Compared to the original ChEC-seq method, the modified version
requires far less amplification. Since MACS3 failed to identify peaks in
data generated from the modified ChEC-seq method, a new peak finder has
been developed specifically for it. There are three functions in the
peak_finder/. callpeaks() is used to identify peaks from BAM files.
goanalysis() is used to make GO (Gene Ontology) term plots from peaks.
bedtomeme() is a wrapper function to perform MEME analysis in R after MEME
Suite is installed locally.