Package: hoodscanR 1.5.0

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:Ning Liu [aut, cre], Jarryd Martin [aut]

hoodscanR_1.5.0.tar.gz
hoodscanR_1.5.0.zip(r-4.5)hoodscanR_1.5.0.zip(r-4.4)hoodscanR_1.5.0.zip(r-4.3)
hoodscanR_1.5.0.tgz(r-4.4-x86_64)hoodscanR_1.5.0.tgz(r-4.4-arm64)hoodscanR_1.5.0.tgz(r-4.3-x86_64)hoodscanR_1.5.0.tgz(r-4.3-arm64)
hoodscanR_1.5.0.tar.gz(r-4.5-noble)hoodscanR_1.5.0.tar.gz(r-4.4-noble)
hoodscanR_1.5.0.tgz(r-4.4-emscripten)hoodscanR_1.5.0.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'))

Peer review:

Bug tracker:https://github.com/davislaboratory/hoodscanr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

    On BioConductor:hoodscanR-1.3.3(bioc 3.20)hoodscanR-1.2.0(bioc 3.19)

    spatialtranscriptomicssinglecellclustering

    5.15 score 4 stars 4 scripts 122 downloads 12 exports 108 dependencies

    Last updated 25 days agofrom:4a8bc84c31. Checks:OK: 9. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKOct 30 2024
    R-4.5-win-x86_64OKOct 31 2024
    R-4.5-linux-x86_64OKOct 30 2024
    R-4.4-win-x86_64OKOct 31 2024
    R-4.4-mac-x86_64OKOct 31 2024
    R-4.4-mac-aarch64OKOct 31 2024
    R-4.3-win-x86_64OKOct 31 2024
    R-4.3-mac-x86_64OKOct 31 2024
    R-4.3-mac-aarch64OKOct 31 2024

    Exports:calcMetricsclustByHoodfindNearCellsmergeByGroupmergeHoodSpeperplexityPermuteplotColocalplotHoodMatplotProbDistplotTissuereadHoodDatascanHoods

    Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbslibcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfilelockfontawesomeforeachfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehighrhtmltoolshttrIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngpurrrR6RANNrappdirsRColorBrewerRcpprjsonrlangrmarkdownRSQLiteS4ArraysS4VectorssassscalesscicoshapeSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc

    A quick start guide to the hoodscanR package

    Ning Liu, Melissa Davis

    Rendered fromQuick_start.Rmdusingknitr::rmarkdownon Oct 30 2024.

    Last update: 2023-09-25
    Started: 2023-08-14

    Readme and manuals

    Help Manual

    Help pageTopics
    Calculate metrics for probability matrixcalcMetrics
    Cluster the probability matrix with K-meansclustByHood clustByHood,matrix-method clustByHood,SpatialExperiment-method
    Find the k-th nearest cells for each cellfindNearCells
    Merge probability matrix based on annotationsmergeByGroup
    Merge probability matrix into SpatialExperiment object.mergeHoodSpe
    Compute p-value for perplexity via permutationperplexityPermute
    Plot heatmap for neighbourhood analysisplotColocal plotColocal,matrix-method plotColocal,SpatialExperiment-method
    Plot probability matrix as a heatmapplotHoodMat plotHoodMat,matrix-method plotHoodMat,SpatialExperiment-method
    Plot probability distributionplotProbDist 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