Package: hoodscanR 1.5.1
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_1.5.1.tar.gz
hoodscanR_1.5.1.zip(r-4.5)hoodscanR_1.5.1.zip(r-4.4)hoodscanR_1.5.1.zip(r-4.3)
hoodscanR_1.5.1.tgz(r-4.4-x86_64)hoodscanR_1.5.1.tgz(r-4.4-arm64)hoodscanR_1.5.1.tgz(r-4.3-x86_64)hoodscanR_1.5.1.tgz(r-4.3-arm64)
hoodscanR_1.5.1.tar.gz(r-4.5-noble)hoodscanR_1.5.1.tar.gz(r-4.4-noble)
hoodscanR_1.5.1.tgz(r-4.4-emscripten)hoodscanR_1.5.1.tgz(r-4.3-emscripten)
hoodscanR.pdf |hoodscanR.html✨
hoodscanR/json (API)
NEWS
| # 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 site:https://davislaboratory.github.io
On BioConductor:hoodscanR-1.5.0(bioc 3.21)hoodscanR-1.4.0(bioc 3.20)
spatialtranscriptomicssinglecellclusteringcpp
Last updated 21 days agofrom:8600f1cedb. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 05 2024 |
| R-4.5-win-x86_64 | OK | Dec 05 2024 |
| R-4.5-linux-x86_64 | OK | Dec 05 2024 |
| R-4.4-win-x86_64 | OK | Dec 05 2024 |
| R-4.4-mac-x86_64 | OK | Dec 05 2024 |
| R-4.4-mac-aarch64 | OK | Dec 05 2024 |
| R-4.3-win-x86_64 | OK | Dec 05 2024 |
| R-4.3-mac-x86_64 | OK | Dec 05 2024 |
| R-4.3-mac-aarch64 | OK | Dec 05 2024 |
Exports:calcMetricsclustByHoodfindNearCellsmergeByGroupmergeHoodSpeperplexityPermuteplotColocalplotHoodMatplotProbDistplotTissuereadHoodDatascanHoods
Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbslibcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfilelockfontawesomeforeachfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehighrhtmltoolshttrIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngpurrrR6RANNrappdirsRColorBrewerRcpprjsonrlangrmarkdownRSQLiteS4ArraysS4VectorssassscalesscicoshapeSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc
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 |
