RChIP-Tech.Rmd: basic statistical analysis and visualization for R-ChIP technology paper (Ref 1).
MDS-MC.Rmd: basic statistical analysis and visualization for mechanism study of MDS by splicing factors mutations (Ref 2).
AverageSlidingWindowGC.pl: GC content of sliding window
GFreq.sh / .pl: consecutive G frequency
profile.sh: generate signal profile (input: .bed6, strand-specific .bw, up/down-stream length)
genomeBinReadsCoverage.sh: bin-wise reads coverage
(1) Chen, L., Chen, J-Y. et. al., Precision R-ChIP Captures R-loops Dynamically Coupled with Transcriptional Pausing at Gene Promoters, Molecular Cell, 2017
(2) Chen, L., Chen, J-Y., Huang, Y-J. et. al., Augmented R-loop is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High Risk Splicing Factor Mutations, Molecular Cell, 2018