Introduction | Installation | Quick start | Data exploration | Neighborhoods scanning | Neighborhoods analysis | Session info
Package: hoodscanR 1.11.0
Ning Liu
hoodscanR: Spatial cellular neighbourhood scanning in R
hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.
Authors:
hoodscanR_1.11.0.tar.gz
hoodscanR_1.11.0.zip(r-4.7)hoodscanR_1.11.0.zip(r-4.6)hoodscanR_1.11.0.zip(r-4.5)
hoodscanR_1.11.0.tgz(r-4.6-x86_64)hoodscanR_1.11.0.tgz(r-4.6-arm64)hoodscanR_1.11.0.tgz(r-4.5-x86_64)hoodscanR_1.11.0.tgz(r-4.5-arm64)
hoodscanR_1.11.0.tar.gz(r-4.7-arm64)hoodscanR_1.11.0.tar.gz(r-4.7-x86_64)hoodscanR_1.11.0.tar.gz(r-4.6-arm64)hoodscanR_1.11.0.tar.gz(r-4.6-x86_64)
hoodscanR_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hoodscanR/json (API)
| # Install 'hoodscanR' in R: |
| install.packages('hoodscanR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davislaboratory/hoodscanr/issues
Pkgdown/docs site:https://davislaboratory.github.io
On BioConductor:hoodscanR-1.11.0(bioc 3.24)hoodscanR-1.10.0(bioc 3.23)
spatialtranscriptomicssinglecellclusteringcpp
Last updated from:09a08af3e3. Checks:1 WARNING, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 194 | ||
| linux-devel-arm64 | OK | 282 | ||
| linux-devel-x86_64 | OK | 393 | ||
| source / vignettes | OK | 264 | ||
| linux-release-arm64 | OK | 293 | ||
| linux-release-x86_64 | OK | 407 | ||
| macos-release-arm64 | OK | 287 | ||
| macos-release-x86_64 | OK | 596 | ||
| macos-oldrel-arm64 | OK | 177 | ||
| macos-oldrel-x86_64 | OK | 426 | ||
| windows-devel | OK | 266 | ||
| windows-release | OK | 270 | ||
| windows-oldrel | OK | 254 | ||
| wasm-release | OK | 161 |
Exports:calcMetricsclustByHoodfindNearCellsmergeByGroupmergeHoodSpeperplexityPermuteplotColocalplotHoodMatplotProbDistplotTissuereadHoodDatascanHoods
Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbslibcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArraydigestdoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachfsgenericsGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehighrhtmltoolshttr2IRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6RANNrappdirsRColorBrewerRcpprjsonrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesscicoSeqinfoshapeSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate metrics for probability matrix | calcMetrics |
| Cluster the probability matrix with K-means | clustByHood clustByHood,matrix-method clustByHood,SpatialExperiment-method |
| Find the k-th nearest cells for each cell | findNearCells |
| Merge probability matrix based on annotations | mergeByGroup |
| Merge probability matrix into SpatialExperiment object. | mergeHoodSpe |
| Compute p-value for perplexity via permutation | perplexityPermute |
| Plot heatmap for neighbourhood analysis | plotColocal plotColocal,matrix-method plotColocal,SpatialExperiment-method |
| Plot probability matrix as a heatmap | plotHoodMat plotHoodMat,matrix-method plotHoodMat,SpatialExperiment-method |
| Plot probability distribution | plotProbDist plotProbDist,matrix-method plotProbDist,SpatialExperiment-method |
| Plot cells based on cell position on tissue. | plotTissue |
| Read cellular position and annotation data into a list object. | readHoodData |
| Scan cellular neighbourhoods. | scanHoods |
