Replication Timing Profiling using DNA Copy Number
A function to calculate Trep values from a sync-seq experiment calcTre...
A function to compare two replication profiles
Load a BED formatted file.
A helper function to create a gemome dataframe
A helper function to create axis ticks and human readable labels.
A function to calculate 'score' ratio between two bed dataframes makeR...
A function to normalise ratio values from 'ratio' column of the provid...
A function to boxplot 'score' column of a BED dataframe, per unique ch...
A function to scatterplot 'score' column of a BED dataframe plotCovera...
plotGenome: plot replication profile.
A function to plot a histogram of supplied ratio vector plotRatio plot...
A function to scatterplot 'Trep' column of a Trep dataframe plotTrep f...
A function to remove single chromosome data from a bed dataframe
A function to remove outliers from the "score" column of a supplied be...
A function to launch Repliscope in interactive mode (Shiny app).
A function to smooth ratio values using cubic smoothing spline smoothR...
A function to remove outliers from the "ratio" column of a supplied ra...
Create, Plot and Compare Replication Timing Profiles. The method is described in Muller et al., (2014) <doi: 10.1093/nar/gkt878>.