Package: DESpace 1.99.2
Peiying Cai
DESpace: DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.
Authors:
DESpace_1.99.2.tar.gz
DESpace_1.99.2.zip(r-4.5)DESpace_1.99.2.zip(r-4.4)DESpace_1.7.0.zip(r-4.3)
DESpace_1.99.2.tgz(r-4.5-any)DESpace_1.99.2.tgz(r-4.4-any)DESpace_1.7.0.tgz(r-4.3-any)
DESpace_1.99.2.tar.gz(r-4.5-noble)DESpace_1.99.2.tar.gz(r-4.4-noble)
DESpace_1.99.2.tgz(r-4.4-emscripten)DESpace_1.7.0.tgz(r-4.3-emscripten)
DESpace.pdf |DESpace.html✨
DESpace/json (API)
NEWS
| # Install 'DESpace' in R: |
| install.packages('DESpace', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/peicai/despace/issues
Pkgdown site:https://peicai.github.io
- LIBD_subset - Subset from the human DLPFC 10x Genomics Visium dataset of the 'spatialLIBD' package
- results_individual_svg - Results from 'individual_svg' function
- results_svg_test - Results from 'svg_test' function
On BioConductor:DESpace-1.99.1(bioc 3.21)DESpace-1.6.1(bioc 3.20)
spatialsinglecellrnaseqtranscriptomicsgeneexpressionsequencingdifferentialexpressionstatisticalmethodvisualization
Last updated 1 days agofrom:3ec00b4fe6. Checks:7 ERROR, 2 FAILURE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | FAIL | Mar 29 2025 |
| R-4.5-win | ERROR | Mar 29 2025 |
| R-4.5-mac | ERROR | Mar 29 2025 |
| R-4.5-linux | ERROR | Mar 29 2025 |
| R-4.4-win | ERROR | Mar 29 2025 |
| R-4.4-mac | ERROR | Mar 29 2025 |
| R-4.4-linux | ERROR | Mar 29 2025 |
| R-4.3-win | OUTDATED | Feb 21 2025 |
| R-4.3-mac | OUTDATED | Feb 21 2025 |
Exports:dsp_testFeaturePlotindividual_dspindividual_svgsvg_testtop_results
Dependencies:abindaskpassassertthatassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclassclassIntclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdplyre1071edgeRfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggnewscaleggplot2gluegoftestgtablehttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrpolyclipproxypurrrR6RColorBrewerRcppRcppEigenrjsonrlangRSQLites2S4ArraysS4VectorsscalesscuttlesfSingleCellExperimentsnowSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsyssystemfontstensorterratibbletidyrtidyselecttweenrUCSC.utilsunitsutf8vctrsviridisLitewithrwkXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| dsp_test | dsp_test |
| FeaturePlot | FeaturePlot |
| individual_dsp | individual_dsp |
| individual_svg | individual_svg |
| Subset from the human DLPFC 10x Genomics Visium dataset of the 'spatialLIBD' package | LIBD_subset |
| Results from 'individual_svg' function | results_individual_svg |
| Results from 'svg_test' function | results_svg_test |
| svg_test | svg_test |
| top_results | top_results |
