Notice to users using OSX with R-devel | Introduction | Usage example | Input data | Preprocessing | Computing cluster assignments | Visualization | Cluster plot | Spatial array plots | Spot-based clustering | Gene-based clustering | The score multiplier | Sub-clustering
Package: SpatialCPie 1.29.0
Joseph Bergenstraahle
SpatialCPie: Cluster analysis of Spatial Transcriptomics data
SpatialCPie is an R package designed to facilitate cluster evaluation for spatial transcriptomics data by providing intuitive visualizations that display the relationships between clusters in order to guide the user during cluster identification and other downstream applications. The package is built around a shiny "gadget" to allow the exploration of the data with multiple plots in parallel and an interactive UI. The user can easily toggle between different cluster resolutions in order to choose the most appropriate visual cues.
Authors:
SpatialCPie_1.29.0.tar.gz
SpatialCPie_1.29.0.zip(r-4.7)SpatialCPie_1.29.0.zip(r-4.6)SpatialCPie_1.29.0.zip(r-4.5)
SpatialCPie_1.29.0.tgz(r-4.6-any)SpatialCPie_1.29.0.tgz(r-4.5-any)
SpatialCPie_1.29.0.tar.gz(r-4.7-any)SpatialCPie_1.29.0.tar.gz(r-4.6-any)
SpatialCPie_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpatialCPie/json (API)
| # Install 'SpatialCPie' in R: |
| install.packages('SpatialCPie', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:SpatialCPie-1.29.0(bioc 3.24)SpatialCPie-1.28.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
transcriptomicsclusteringrnaseqsoftware
Last updated from:de961a4a55. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 198 | ||
| linux-devel-x86_64 | NOTE | 297 | ||
| source / vignettes | OK | 242 | ||
| linux-release-x86_64 | NOTE | 320 | ||
| macos-release-arm64 | NOTE | 218 | ||
| macos-oldrel-arm64 | NOTE | 177 | ||
| windows-devel | NOTE | 207 | ||
| windows-release | NOTE | 201 | ||
| windows-oldrel | NOTE | 196 | ||
| wasm-release | OK | 175 |
Exports:parseSpotFilerunCPie
Dependencies:abindbase64encBiobaseBiocGenericsbitbit64bslibcachemclicliprcolorspacecommonmarkcpp11crayondata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsGenomicRangesggforceggiraphggplot2ggrepelgluegtablehighrhmshtmltoolshtmlwidgetshttpuvigraphIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclelpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeotelpillarpkgconfigpolyclipprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoshinyshinycssloadersshinyjsshinyWidgetssourcetoolsSparseArraystringistringrSummarizedExperimentsystemfontstibbletidyrtidyselecttinytextweenrtzdbutf8vctrsviridisLitevroomwithrxfunxtableXVectoryamlzeallot
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SpatialCPie: Cluster analysis of Spatial Transcriptomics data | SpatialCPie-package SpatialCPie |
| Parse spot detector output | parseSpotFile |
| Run SpatialCPie | runCPie |
