Package: SPACO 1.0.3
SPACO: Spatial Component Analysis for Spatial Sequencing Data
Spatial components offer tools for dimension reduction and spatially variable gene detection for high dimensional spatial transcriptomics data. Construction of a projection onto low-dimensional feature space of spatially dependent metagenes offers pre-processing to clustering, testing for spatial variability and denoising of spatial expression patterns. For more details, see Koehler et al. (2026) <doi:10.1093/bioinformatics/btag052>.
Authors:
SPACO_1.0.3.tar.gz
SPACO_1.0.3.zip(r-4.7-x86_64)SPACO_1.0.3.zip(r-4.7-arm64)SPACO_1.0.3.zip(r-4.6-x86_64)SPACO_1.0.3.zip(r-4.6-arm64)SPACO_1.0.3.zip(r-4.5-x86_64)
SPACO_1.0.3.tgz(r-4.6-x86_64)SPACO_1.0.3.tgz(r-4.6-arm64)SPACO_1.0.3.tgz(r-4.5-x86_64)SPACO_1.0.3.tgz(r-4.5-arm64)
SPACO_1.0.3.tar.gz(r-4.7-arm64)SPACO_1.0.3.tar.gz(r-4.7-x86_64)SPACO_1.0.3.tar.gz(r-4.6-arm64)SPACO_1.0.3.tar.gz(r-4.6-x86_64)
SPACO_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SPACO/json (API)
| # Install 'SPACO' in R: |
| install.packages('SPACO', repos = c('https://koehlibert.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:eb049ad0d2. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 191 | ||
| linux-devel-x86_64 | OK | 225 | ||
| source / vignettes | OK | 414 | ||
| linux-release-arm64 | OK | 350 | ||
| linux-release-x86_64 | OK | 455 | ||
| macos-release-arm64 | OK | 201 | ||
| macos-release-x86_64 | OK | 422 | ||
| macos-oldrel-arm64 | OK | 180 | ||
| macos-oldrel-x86_64 | OK | 427 | ||
| windows-devel-arm64 | OK | 493 | ||
| windows-devel-x86_64 | OK | 293 | ||
| windows-release-arm64 | OK | 424 | ||
| windows-release-x86_64 | OK | 480 | ||
| windows-oldrel-x86_64 | OK | 202 | ||
| wasm-release | OK | 287 |
Exports:create_SpaCoObject_from_KNNdenoise_profilesdenoised_projection_ploteigenMapMatMultfeature_plotread_10x_for_spacoset_projectionseurat_to_spacoSpaCoSpaco_plotSpaCoObjectspacs_to_seuratsubset_non_neighbour_cellsSVGTest
Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggforceggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsrARPACKRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppThreadRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortibbletidyrtidyselecttinytextweenrutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| create_SpaCoObject_from_KNN | create_SpaCoObject_from_KNN |
| computes smoothed gene profiles of genes present in the data. | denoise_profiles |
| Plot denoised gene expression | denoised_projection_plot |
| Multiply two matrices using Eigen library | eigenMapMatMult |
| Plot gene expression | feature_plot |
| Read in 10x Visium spatial transcriptomics data | read_10x_for_spaco |
| Set projections of Spaco Object | set_projection |
| Wrapper to transform existing Seurat object into an SpaCoObject. | seurat_to_spaco |
| SpaCo | SpaCo |
| Plot SPaCo meta genes. | Spaco_plot |
| Create a constructor function that creates an object of class SpaCoObject | SpaCoObject |
| transfer computed spatial components to existing Seurat object. | spacs_to_seurat |
| Filtering function to remove cells without neighbours in defined distance from existing Seurat object to be conformable with existing SpaCoObject. | subset_non_neighbour_cells |
| Compute the spatial variable genes of a SpaCoObject after runinng runSCA | SVGTest |