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

Repliscope_1.1.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Repliscope/json (API)

# Install 'Repliscope' in R:

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

Datasets:

Dbf4myc - Sequence read coverage ratios for S.cerevisiae Dbf4-9myc sample.
guide - Guide dataframe for plotting smoothed sortSeq data
MFAseq - Replication profile for wild type DS2 H.volcanii
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
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

On CRAN:

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

3.15 score 28 scripts 287 downloads 1 mentions 17 exports 52 dependencies

Last updated from:4513be718c. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	166
source / vignettes	OK	199
linux-release-x86_64	OK	183
macos-release-arm64	OK	138
macos-oldrel-arm64	OK	147
windows-devel	OK	130
windows-release	OK	109
windows-oldrel	OK	98
wasm-release	OK	117

Exports:calcTrep compareRatios loadBed makeGenome makeLabels makeRatio normaliseRatio plotBed plotCoverage plotGenome plotRatio plotTrep rmChr rmOutliers runGUI smoothRatio trimRatio

Dependencies:base64enc bslib cachem cli colourpicker commonmark cpp11 digest evaluate farver fastmap fontawesome fs ggplot2 glue gtable highr htmltools htmlwidgets httpuv isoband jquerylib jsonlite knitr labeling later lifecycle magrittr memoise mime miniUI otel promises R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales shiny shinyjs sourcetools tinytex vctrs viridisLite withr xfun xtable yaml

Repliscope

Rendered fromRepliscope.Rmdusingknitr::rmarkdown

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

Citation

Readme and manuals

Help Manual

Help page	Topics
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 profiles	compareRatios
Sequence read coverage ratios for S.cerevisiae Dbf4-9myc sample.	Dbf4myc
Guide dataframe for plotting smoothed sortSeq data	guide
Load a BED formatted file.	loadBed
A helper function to create a gemome dataframe	makeGenome
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.volcanii	MFAseq
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 dataframe	rmChr
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 information	sacCer3
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 samples	sortSeq
Replication profiles budding yeast arrest-release samples	syncSeq
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 W303	W303
Sequence read coverage for wild type S.cerevisiae W303 non-replicating sample.	W303_G2
Sequence read coverage for wild type S.cerevisiae W303 replicating sample	W303_S
Normalised sequence read coverage ratios for wild type S.cerevisiae W303	W303norm

Package: Repliscope 1.1.1

Repliscope: Replication Timing Profiling using DNA Copy Number

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)