Package: SpatialDecon 1.15.0

Maddy Griswold

SpatialDecon: Deconvolution of mixed cells from spatial and/or bulk gene expression data

Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.

Authors:Maddy Griswold [cre, aut], Patrick Danaher [aut]

SpatialDecon_1.15.0.tar.gz
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SpatialDecon_1.15.0.tgz(r-4.4-any)SpatialDecon_1.15.0.tgz(r-4.3-any)
SpatialDecon_1.15.0.tar.gz(r-4.5-noble)SpatialDecon_1.15.0.tar.gz(r-4.4-noble)
SpatialDecon_1.15.0.tgz(r-4.4-emscripten)
SpatialDecon.pdf |SpatialDecon.html✨
SpatialDecon/json (API)
NEWS

# Install 'SpatialDecon' in R:

install.packages('SpatialDecon', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nanostring-biostats/spatialdecon/issues

Datasets:

cellcols - Default colors for the cell types in the safeTME matrix
mean.resid.sd - Genes' biological variability in immune deconvolution from TCGA.
mini_geomx_dataset - Small example GeoMx data
mini_singleCell_dataset - Mini human colon single cell dataset
nsclc - Large example GeoMx data
safeTME - SafeTME matrix
safeTME.matches - Mapping from granularly-defined cell populations to broaded cell populations

On BioConductor:SpatialDecon-1.15.0(bioc 3.20)SpatialDecon-1.14.0(bioc 3.19)

bioconductor-package

14 exports 1.31 score 136 dependencies

Last updated 2 months agofrom:091cec3fde

Exports:collapseCellTypes create_profile_matrix derive_GeoMx_background download_profile_matrix florets mergeTumorIntoX reverseDecon runCollapseCellTypes runErrorModel runMergeTumorIntoX runReverseDecon runspatialdecon spatialdecon TIL_barplot

Dependencies:askpass backports base64enc beeswarm Biobase BiocGenerics Biostrings bit bit64 boot broom broom.helpers bslib cachem cellranger cli clipr codetools colorspace cpp11 crayon curl data.table digest dotCall64 dplyr EnvStats evaluate fansi farver fastmap fontawesome forcats fs future future.apply generics GenomeInfoDb GenomeInfoDbData GeomxTools GGally ggbeeswarm ggiraph ggplot2 ggstats ggthemes globals glue gtable haven highr hms htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling labelled lattice lifecycle listenv lme4 lmerTest logNormReg magrittr MASS Matrix memoise mgcv mime minqa munsell NanoStringNCTools nlme nloptr nortest numDeriv openssl parallelly patchwork pheatmap pillar pkgconfig plyr prettyunits progress progressr purrr R.cache R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen readr readxl rematch repmis reshape2 rjson rlang rmarkdown S4Vectors sass scales SeuratObject sp spam stringi stringr sys systemfonts tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 uuid vctrs vipor viridisLite vroom withr xfun XVector yaml zlibbioc

Use of SpatialDecon in a large GeoMx dataset with GeomxTools

Rendered fromSpatialDecon_vignette_NSCLC.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-10-30
Started: 2021-10-13

Use of SpatialDecon in a small GeoMx dataset

Rendered fromSpatialDecon_vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-01-11
Started: 2020-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SpatialDecon: A package for estimating mixed cell type abundance in the regions of spatially-resolved gene expression studies	SpatialDecon-package
Default colors for the cell types in the safeTME matrix	cellcols
Collapse related cell types within a deconvolution result	collapseCellTypes
Create Custom Cell Profile Matrix	create_profile_matrix
Derive background at the scale of the normalized data for GeoMx data	derive_GeoMx_background
Download a cell profile matrix	download_profile_matrix
Draw coxcomb plots as points in a graphics window	florets
Genes' biological variability in immune deconvolution from TCGA.	mean.resid.sd
Estimate a tumor-specific profile and merge it with the pre-specified cell profile matrix (X)	mergeTumorIntoX
Small example GeoMx data	mini_geomx_dataset
Mini human colon single cell dataset	mini_singleCell_dataset
Large example GeoMx data	nsclc
Reverse deconvolution	reverseDecon
Run collapseCellTypes	runCollapseCellTypes runCollapseCellTypes,NanoStringGeoMxSet-method
Apply error model to estimate technical SD from raw counts	runErrorModel
Run MergeTumorIntoX	runMergeTumorIntoX runMergeTumorIntoX,NanoStringGeoMxSet-method
Run Reversedecon	runReverseDecon runReverseDecon,NanoStringGeoMxSet-method
Run spatialdecon	runspatialdecon runspatialdecon,NanoStringGeoMxSet-method runspatialdecon,Seurat-method
SafeTME matrix	safeTME
Mapping from granularly-defined cell populations to broaded cell populations	safeTME.matches
Mixed cell deconvolution of spatiall-resolved gene expression data	spatialdecon
Barplot of abundance estimates	TIL_barplot