Package: Repliscope 1.1.1

Repliscope: Replication Timing Profiling using DNA Copy Number

Create, Plot and Compare Replication Timing Profiles. The method is described in Muller et al., (2014) <doi:10.1093/nar/gkt878>.

Authors:Dzmitry G Batrakou

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NEWS

# Install 'Repliscope' in R:
install.packages('Repliscope', repos = c('https://dzmitrygb.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Dbf4myc - Sequence read coverage ratios for S.cerevisiae Dbf4-9myc sample.
  • MFAseq - Replication profile for wild type DS2 H.volcanii
  • TrepDF - Trep data calculated from syncSeq[["data"]]
  • W303 - Sequence read coverage ratios for wild type S.cerevisiae W303
  • W303_G2 - Sequence read coverage for wild type S.cerevisiae W303 non-replicating sample.
  • W303_S - Sequence read coverage for wild type S.cerevisiae W303 replicating sample
  • W303norm - Normalised sequence read coverage ratios for wild type S.cerevisiae W303
  • guide - Guide dataframe for plotting smoothed sortSeq data
  • sacCer3 - S.cerevisiae genome information
  • sortSeq - Replication profiles for wild type and Dbf4-9myc S.cerevisiae samples
  • syncSeq - Replication profiles budding yeast arrest-release samples

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

17 exports 0.36 score 62 dependencies 1 mentions 27 scripts 277 downloads

Last updated 2 years agofrom:4513be718c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 30 2024
R-4.5-winOKAug 30 2024
R-4.5-linuxOKAug 30 2024
R-4.4-winOKAug 30 2024
R-4.4-macOKAug 30 2024
R-4.3-winOKAug 30 2024
R-4.3-macOKAug 30 2024

Exports:calcTrepcompareRatiosloadBedmakeGenomemakeLabelsmakeRationormaliseRatioplotBedplotCoverageplotGenomeplotRatioplotTreprmChrrmOutliersrunGUIsmoothRatiotrimRatio

Dependencies:base64encbslibcachemclicolorspacecolourpickercommonmarkcrayondigestevaluatefansifarverfastmapfontawesomefsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnlmepillarpkgconfigpromisesR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesshinyshinyjssourcetoolstibbletinytexutf8vctrsviridisLitewithrxfunxtableyaml

Repliscope

Dzmitry G Batrakou

Rendered fromRepliscope.Rmdusingknitr::rmarkdownon Aug 30 2024.

Last update: 2019-07-15
Started: 2019-02-06

Readme and manuals

Help Manual

Help pageTopics
A function to calculate Trep values from a sync-seq experiment calcTrep function fits a Boltzman sigmoid function into relative copy number datapoints for every genomic bin of the provided sync-seq merged dataframe. It then extracts time at which half of the cells have this genomic bin replicated (Trep). The output of the function is a dataframe containing Trep and TrepErr data for every genomic bin in a BED-like format.calcTrep
A function to compare two replication profilescompareRatios
Sequence read coverage ratios for S.cerevisiae Dbf4-9myc sample.Dbf4myc
Guide dataframe for plotting smoothed sortSeq dataguide
Load a BED formatted file.loadBed
A helper function to create a gemome dataframemakeGenome
A helper function to create axis ticks and human readable labels.makeLabels
A function to calculate 'score' ratio between two bed dataframes makeRatio merges two supplied bed dataframes, calculates ratio of their "score" values normalises the ratio by the 'score' sums.makeRatio
Replication profile for wild type DS2 H.volcaniiMFAseq
A function to normalise ratio values from 'ratio' column of the provided dataframe to fit biologically-relevant scale. It scales values either using supplied 'rFactor' value or automatically to best fit 1 to 2 scale (the upper limit of the scale may be adjusted with the upperLimit parameter). Normalisation factor used is stored in 'ratioFactor' column and also passed as the dataframe comment. To extract it, use 'attributes(mergedBed)$comment'normaliseRatio normalizeRatio
A function to boxplot 'score' column of a BED dataframe, per unique chromosome name in the 'chrom' column. The resulting plot also highlights outliers based on the inter quartile range (IQR). The genome wide median is plotted as a pink line through the boxplots.plotBed
A function to scatterplot 'score' column of a BED dataframe plotCoverage function plots values in the 'score' column of the supplied bed dataframe as a function of chromosome coordinates. The genome wide median is plotted as a pink line.plotCoverage
plotGenome: plot replication profile.plotGenome
A function to plot a histogram of supplied ratio vector plotRatio plots histogram of values in a supplied vector using ggplot2 and highlights interval between 1 and 2 in green.plotRatio
A function to scatterplot 'Trep' column of a Trep dataframe plotTrep function plots values in the 'Trep' column of the supplied dataframe as a function of chromosome coordinates. The genome wide median is plotted as a pink line.plotTrep
A function to remove single chromosome data from a bed dataframermChr
A function to remove outliers from the "score" column of a supplied bed dataframe There are three methods: max, IQR and median. Max is used to remove 1 or more maximum values; IQR uses interquartile range to detect outliers, while median method can be used to remove data based on genome-wide median.rmOutliers
A function to launch Repliscope in interactive mode (Shiny app).runGUI
S.cerevisiae genome informationsacCer3
A function to smooth ratio values using cubic smoothing spline smoothRatio function splits values from 'ratio' column by chromosome and based the supplied 'groupMin' and 'split' parameters and then applies smooth.spline() function from R stats package. The supplied dataframe may contain multiple ratios, i.e. ratios produced using multiple replicating samples and/or multiple non-replicating samples. This must be reflected in 'name.rep' and 'name.nonRep' columns. In other words, different ratio dataframes may be merged using rbind() function before calling smoothRatio() function.smoothRatio
Replication profiles for wild type and Dbf4-9myc S.cerevisiae samplessortSeq
Replication profiles budding yeast arrest-release samplessyncSeq
Trep data calculated from syncSeq[["data"]]TrepDF
A function to remove outliers from the "ratio" column of a supplied ratio dataframe trimRatio is applied to the calculated ratio of read counts from a replicating to a non-replicating samples.trimRatio
Sequence read coverage ratios for wild type S.cerevisiae W303W303
Sequence read coverage for wild type S.cerevisiae W303 non-replicating sample.W303_G2
Sequence read coverage for wild type S.cerevisiae W303 replicating sampleW303_S
Normalised sequence read coverage ratios for wild type S.cerevisiae W303W303norm