Package: timescape 1.31.0

Maia Smith

timescape: Patient Clonal Timescapes

TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.

Authors:Maia Smith [aut, cre]

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timescape.pdf |timescape.html
timescape/json (API)

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

Peer review:

On BioConductor:timescape-1.31.0(bioc 3.21)timescape-1.30.0(bioc 3.20)

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

visualizationbiomedicalinformatics

4.00 score 7 scripts 224 downloads 1 mentions 14 exports 41 dependencies

Last updated 3 months agofrom:9a6dbe7316. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winWARNINGJan 29 2025
R-4.5-macWARNINGJan 29 2025
R-4.5-linuxWARNINGJan 29 2025
R-4.4-winWARNINGJan 29 2025
R-4.4-macWARNINGJan 29 2025
R-4.3-winWARNINGJan 29 2025
R-4.3-macWARNINGJan 29 2025

Exports:checkAlphacheckClonalPrevcheckCloneColourscheckGtypePositioningcheckMinDimscheckPertscheckRequiredInputscheckTreeEdgesgetMutationsDataprocessUserDatarenderTimescapereplaceSpacestimescapetimescapeOutput

Dependencies:base64encbslibcachemclidigestdplyrevaluatefansifastmapfontawesomefsgenericsgluegtoolshighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimepillarpkgconfigR6rappdirsrlangrmarkdownsassstringistringrtibbletidyselecttinytexutf8vctrswithrxfunyaml

TimeScape vignette

Rendered fromtimescape_vignette.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2018-08-30
Started: 2017-02-11

Readme and manuals

Help Manual

Help pageTopics
TimeScapetimescape
Widget output function for use in ShinycheckAlpha checkClonalPrev checkCloneColours checkGtypePositioning checkMinDims checkPerts checkRequiredInputs checkTreeEdges getMutationsData processUserData renderTimescape replaceSpaces timescapeOutput