Package: spatialDE 1.13.0

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:Davide Corso [aut], Milan Malfait [aut], Lambda Moses [aut], Gabriele Sales [cre]

spatialDE_1.13.0.tar.gz
spatialDE_1.13.0.zip(r-4.5)spatialDE_1.13.0.zip(r-4.4)spatialDE_1.13.0.zip(r-4.3)
spatialDE_1.13.0.tgz(r-4.5-any)spatialDE_1.13.0.tgz(r-4.4-any)spatialDE_1.13.0.tgz(r-4.3-any)
spatialDE_1.13.0.tar.gz(r-4.5-noble)spatialDE_1.13.0.tar.gz(r-4.4-noble)
spatialDE_1.13.0.tgz(r-4.4-emscripten)spatialDE_1.13.0.tgz(r-4.3-emscripten)
spatialDE.pdf |spatialDE.html✨
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-1.13.0(bioc 3.21)spatialDE-1.12.0(bioc 3.20)

software transcriptomics python spatial-data wrapper

4.76 score 3 stars 16 scripts 264 downloads 2 mentions 11 exports 90 dependencies

Last updated 4 months agofrom:03b4e0efd8. Checks:8 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Feb 28 2025
R-4.5-win	ERROR	Feb 28 2025
R-4.5-mac	ERROR	Feb 28 2025
R-4.5-linux	ERROR	Feb 28 2025
R-4.4-win	ERROR	Feb 28 2025
R-4.4-mac	ERROR	Feb 28 2025
R-4.3-win	ERROR	Feb 28 2025
R-4.3-mac	ERROR	Feb 28 2025

Exports:FSV_sig mockSVG model_search modelSearch multiGenePlots regress_out run spatial_patterns spatialDE spatialPatterns stabilize

Dependencies:abind askpass backports basilisk basilisk.utils Biobase BiocFileCache BiocGenerics bit bit64 blob cachem checkmate cli colorspace cpp11 crayon curl DBI dbplyr DelayedArray dir.expiry dplyr fansi farver fastmap filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel glue gridExtra gtable here httr IRanges isoband jsonlite labeling lattice lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png purrr R6 rappdirs RColorBrewer Rcpp RcppTOML reticulate rjson rlang rprojroot RSQLite S4Arrays S4Vectors scales SingleCellExperiment SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot Fraction Spatial Variance vs Q-value	FSV_sig
Mouse Olfactory Bulb sample metadata	MOB_sample_info
Generate count matrix for spatially variable genes.	mockSVG
Compare model fits with different models	model_search
Classify Spatially Variable Genes to interpretable fitting classes	modelSearch modelSearch,matrix-method modelSearch,SpatialExperiment-method
Plot Spatial Patterns of Multiple Genes	multiGenePlots multiGenePlots,matrix-method multiGenePlots,SpatialExperiment-method
Regress out library size effect	regress_out
Mouse Olfactory Bulb spatial gene expression data	Rep11_MOB_0
Perform SpatialDE test	run
Group spatially variable genes into spatial patterns using automatic expression histology (AEH)	spatial_patterns
Find spatially variable genes with SpatialDE	spatialDE spatialDE,matrix-method spatialDE,SpatialExperiment-method
Automatic expression histology in SpatialDE	spatialPatterns spatialPatterns,matrix-method spatialPatterns,SpatialExperiment-method
Stabilize variance of counts	stabilize