Introduction | Installation | Example: Mouse Olfactory Bulb | Load data | Filter out pratically unobserved genes | Get total_counts for every spot | Get coordinates from MOB_sample_info | stabilize | regress_out | run | model_search | spatial_patterns | Plots | Plot Spatial Patterns of Multiple Genes | Plot Fraction Spatial Variance vs Q-value | SpatialExperiment integration | Plot Spatial Patterns of Multiple Genes (using SpatialExperiment object) | Classify spatially variable genes with model_search and spatial_patterns | sessionInfo
Package: spatialDE 1.19.0
Gabriele Sales
spatialDE: R wrapper for SpatialDE
SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.
Authors:
spatialDE_1.19.0.tar.gz
spatialDE_1.19.0.zip(r-4.7-any)spatialDE_1.19.0.zip(r-4.6-any)spatialDE_1.19.0.zip(r-4.5-any)
spatialDE_1.19.0.tgz(r-4.6-any)spatialDE_1.19.0.tgz(r-4.5-any)
spatialDE_1.19.0.tar.gz(r-4.7-any)spatialDE_1.19.0.tar.gz(r-4.6-any)
spatialDE_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
spatialDE/json (API)
| # Install 'spatialDE' in R: |
| install.packages('spatialDE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sales-lab/spatialde/issues
Datasets:
- MOB_sample_info - Mouse Olfactory Bulb sample metadata
- Rep11_MOB_0 - Mouse Olfactory Bulb spatial gene expression data
On BioConductor:spatialDE-1.19.0(bioc 3.24)spatialDE-1.18.0(bioc 3.23)
softwaretranscriptomicspythonspatial-datawrapper
Last updated from:59649f3313. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 183 | ||
| linux-devel-x86_64 | NOTE | 1164 | ||
| source / vignettes | OK | 1140 | ||
| linux-release-x86_64 | NOTE | 1157 | ||
| macos-release-arm64 | NOTE | 667 | ||
| macos-oldrel-arm64 | NOTE | 801 | ||
| windows-devel | NOTE | 352 | ||
| windows-release | NOTE | 391 | ||
| windows-oldrel | NOTE | 357 | ||
| wasm-release | OK | 147 |
Exports:FSV_sigmockSVGmodel_searchmodelSearchmultiGenePlotsregress_outrunspatial_patternsspatialDEspatialPatternsstabilize
Dependencies:abindaskpassbackportsbasiliskBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemcheckmateclicpp11curlDBIdbplyrDelayedArraydir.expirydplyrfarverfastmapfilelockgenericsGenomicRangesggplot2ggrepelgluegridExtragtableherehttr2IRangesisobandjsonlitelabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRcppTOMLreticulaterjsonrlangrprojrootRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
