Introduction | Installation | Example Code | Compute spRI and spARI | Use spatial coordinates as input | Use a distance matrix as input | Use a sparse distance matrix as input | Use an adjacency matrix as input | Conducting hypothesis testing | Support for SpatialExperiment objects | Session information
Package: spARI 1.3.0
Yinqiao Yan
spARI: Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering
The R package used in the manuscript "Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering".
Authors:
spARI_1.3.0.tar.gz
spARI_1.3.0.zip(r-4.7)spARI_1.3.0.zip(r-4.6)spARI_1.3.0.zip(r-4.5)
spARI_1.3.0.tgz(r-4.6-x86_64)spARI_1.3.0.tgz(r-4.6-arm64)spARI_1.3.0.tgz(r-4.5-x86_64)spARI_1.3.0.tgz(r-4.5-arm64)
spARI_1.3.0.tar.gz(r-4.7-arm64)spARI_1.3.0.tar.gz(r-4.7-x86_64)spARI_1.3.0.tar.gz(r-4.6-arm64)spARI_1.3.0.tar.gz(r-4.6-x86_64)
spARI_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spARI/json (API)
| # Install 'spARI' in R: |
| install.packages('spARI', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- spARI_example_data - Example data for spARI
On BioConductor:spARI-1.3.0(bioc 3.24)spARI-1.2.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
clusteringdataimportgeneexpressiontranscriptomicsspatialsoftwarecpp
Last updated from:f33e3d06f3. Checks:12 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 183 | ||
| linux-devel-arm64 | NOTE | 278 | ||
| linux-devel-x86_64 | NOTE | 296 | ||
| source / vignettes | OK | 270 | ||
| linux-release-arm64 | NOTE | 246 | ||
| linux-release-x86_64 | NOTE | 320 | ||
| macos-release-arm64 | NOTE | 182 | ||
| macos-release-x86_64 | NOTE | 493 | ||
| macos-oldrel-arm64 | NOTE | 147 | ||
| macos-oldrel-x86_64 | NOTE | 322 | ||
| windows-devel | NOTE | 283 | ||
| windows-release | NOTE | 280 | ||
| windows-oldrel | NOTE | 225 | ||
| wasm-release | OK | 149 |
Exports:generate_gs_pairs_intgenerate_sg_pairs_intperm_testspARI
Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclicodetoolscpp11curlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2IRangeslambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsRcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generate object pairs (gs pairs) | generate_gs_pairs_int |
| Generate object pairs (sg pairs) | generate_sg_pairs_int |
| The function perm_test is the main function to carry out the hypothesis test procedure proposed in the paper. | perm_test |
| The function spARI is the main function to calculate spRI and spARI values proposed in the paper. | spARI |
| Example data for spARI | spARI_example_data |
