| calcTrep | A function to calculate Trep values from a sync-seq... |
| compareRatios | A function to compare two replication profiles |
| Dbf4myc | Sequence read coverage ratios for S.cerevisiae Dbf4-9myc... |
| guide | Guide dataframe for plotting smoothed sortSeq data |
| loadBed | Load a BED formatted file. |
| makeGenome | A helper function to create a gemome dataframe |
| makeLabels | A helper function to create axis ticks and human readable... |
| makeRatio | A function to calculate 'score' ratio between two bed... |
| MFAseq | Replication profile for wild type DS2 H.volcanii |
| normaliseRatio | A function to normalise ratio values from 'ratio' column of... |
| plotBed | A function to boxplot 'score' column of a BED dataframe, per... |
| plotCoverage | A function to scatterplot 'score' column of a BED dataframe... |
| plotGenome | plotGenome: plot replication profile. |
| plotRatio | A function to plot a histogram of supplied ratio vector... |
| plotTrep | A function to scatterplot 'Trep' column of a Trep dataframe... |
| rmChr | A function to remove single chromosome data from a bed... |
| rmOutliers | A function to remove outliers from the "score" column of a... |
| runGUI | A function to launch Repliscope in interactive mode (Shiny... |
| sacCer3 | S.cerevisiae genome information |
| smoothRatio | A function to smooth ratio values using cubic smoothing... |
| sortSeq | Replication profiles for wild type and Dbf4-9myc S.cerevisiae... |
| syncSeq | Replication profiles budding yeast arrest-release samples |
| TrepDF | Trep data calculated from syncSeq[["data"]] |
| trimRatio | A function to remove outliers from the "ratio" column of a... |
| W303 | Sequence read coverage ratios for wild type S.cerevisiae W303 |
| W303_G2 | Sequence read coverage for wild type S.cerevisiae W303... |
| W303norm | Normalised sequence read coverage ratios for wild type... |
| W303_S | Sequence read coverage for wild type S.cerevisiae W303... |
