Package: cellscape 1.29.0
Shixiang Wang
cellscape: Explores single cell copy number profiles in the context of a single cell tree
CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.
Authors:
cellscape_1.29.0.tar.gz
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cellscape.pdf |cellscape.html✨
cellscape/json (API)
| # Install 'cellscape' in R: |
| install.packages('cellscape', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:cellscape-1.29.0(bioc 3.20)cellscape-1.28.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:373fa9ec02
Exports:cellscapecellscapeOutputcheckAlphacheckClonalPrevcheckCloneColourscheckGtypePositioningcheckMinDimscheckPertscheckRequiredInputscheckTreeEdgesdfs_treefindModegetMutationsDatarenderCnvTreereplaceSpaces
Dependencies:base64encbslibcachemclidigestdplyrevaluatefansifastmapfontawesomefsgenericsgluegtoolshighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimepillarpkgconfigplyrR6rappdirsRcppreshape2rlangrmarkdownsassstringistringrtibbletidyselecttinytexutf8vctrswithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CellScape | cellscape |
| Get depth first search of a tree | cellscapeOutput checkAlpha checkClonalPrev checkCloneColours checkGtypePositioning checkMinDims checkPerts checkRequiredInputs checkTreeEdges dfs_tree findMode getChromBounds getChromBoxInfo getCNVHeatmapForEachSC getEmptyGrid getGenomeLength getMutationsData getMutOrder getNBPPerPixel getTargetedHeatmapForEachSC processUserData renderCnvTree replaceSpaces |
