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

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)

software transcriptomics python spatial-data wrapper

6.76 score 3 stars 159 scripts 463 downloads 2 mentions 11 exports 79 dependencies

Last updated from:59649f3313. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	159
linux-devel	NOTE	1180
source / vignettes	OK	1126
linux-release	NOTE	815
macos-release	NOTE	835
macos-oldrel	NOTE	951
windows-devel	NOTE	280
windows-release	NOTE	343
windows-oldrel	NOTE	338
wasm-release	OK	131

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

Dependencies:abind askpass backports basilisk Biobase BiocFileCache BiocGenerics bit bit64 blob cachem checkmate cli cpp11 curl DBI dbplyr DelayedArray dir.expiry dplyr farver fastmap filelock generics GenomicRanges ggplot2 ggrepel glue gridExtra gtable here httr2 IRanges isoband jsonlite labeling lattice lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig png purrr R6 rappdirs RColorBrewer Rcpp RcppTOML reticulate rjson rlang rprojroot RSQLite S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

Introduction to spatialDE

Rendered fromspatialDE.Rmdusingknitr::rmarkdown

Last update: 2021-08-26
Started: 2021-02-14

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