Package: DESpace 1.7.0
Peiying Cai
DESpace: DESpace: a framework to discover spatially variable genes
Intuitive framework for identifying spatially variable genes (SVGs) 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. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates.
Authors:
DESpace_1.7.0.tar.gz
DESpace_1.7.0.zip(r-4.5)DESpace_1.7.0.zip(r-4.4)DESpace_1.7.0.zip(r-4.3)
DESpace_1.7.0.tgz(r-4.4-any)DESpace_1.7.0.tgz(r-4.3-any)
DESpace_1.7.0.tar.gz(r-4.5-noble)DESpace_1.7.0.tar.gz(r-4.4-noble)
DESpace_1.7.0.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
- LIBD_subset - Subset from the human DLPFC 10x Genomics Visium dataset of the 'spatialLIBD' package
- results_DESpace_test - Results from 'DESpace_test' function
- results_individual_test - Results from 'individual_test' function
On BioConductor:DESpace-1.5.0(bioc 3.20)DESpace-1.4.0(bioc 3.19)
spatialsinglecellrnaseqtranscriptomicsgeneexpressionsequencingdifferentialexpressionstatisticalmethodvisualization
Last updated 23 days agofrom:2b11443ad6. Checks:OK: 4 NOTE: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | OK | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | OK | Oct 30 2024 |
| R-4.3-mac | OK | Oct 30 2024 |
Exports:DESpace_testFeaturePlotindividual_testtop_results
Dependencies:abindaskpassassertthatbackportsBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootbroomcachemcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivdoBydplyredgeRfansifarverfastmapfilelockformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggnewscaleggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalme4locfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigplogrpolyclippolynompurrrquantregR6RColorBrewerRcppRcppEigenrjsonrlangRSQLiterstatixS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraySparseMSpatialExperimentstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidyrtidyselecttweenrUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DESpace_test | DESpace_test |
| FeaturePlot | FeaturePlot |
| individual_test | individual_test |
| Subset from the human DLPFC 10x Genomics Visium dataset of the 'spatialLIBD' package | LIBD_subset |
| Results from 'DESpace_test' function | results_DESpace_test |
| Results from 'individual_test' function | results_individual_test |
| top_results | top_results |
