Package: SpatialDecon 1.17.0
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:
SpatialDecon_1.17.0.tar.gz
SpatialDecon_1.17.0.zip(r-4.5)SpatialDecon_1.17.0.zip(r-4.4)SpatialDecon_1.17.0.zip(r-4.3)
SpatialDecon_1.17.0.tgz(r-4.4-any)SpatialDecon_1.17.0.tgz(r-4.3-any)
SpatialDecon_1.17.0.tar.gz(r-4.5-noble)SpatialDecon_1.17.0.tar.gz(r-4.4-noble)
SpatialDecon_1.17.0.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
- 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-1.17.0(bioc 3.21)SpatialDecon-1.16.0(bioc 3.20)
immunooncologyfeatureextractiongeneexpressiontranscriptomicsspatial
Last updated 2 months agofrom:7d7d8396ee. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 23 2024 |
| R-4.5-win | NOTE | Nov 23 2024 |
| R-4.5-linux | NOTE | Nov 23 2024 |
| R-4.4-win | NOTE | Nov 23 2024 |
| R-4.4-mac | NOTE | Nov 23 2024 |
| R-4.3-win | NOTE | Nov 23 2024 |
| R-4.3-mac | NOTE | Nov 23 2024 |
Exports:collapseCellTypescreate_profile_matrixderive_GeoMx_backgrounddownload_profile_matrixfloretsmergeTumorIntoXreverseDeconrunCollapseCellTypesrunErrorModelrunMergeTumorIntoXrunReverseDeconrunspatialdeconspatialdeconTIL_barplot
Dependencies:askpassbase64encbeeswarmBiobaseBiocGenericsBiostringsbootbslibcachemcellrangerclicodetoolscolorspacecpp11crayoncurldata.tabledigestdotCall64dplyrEnvStatsevaluatefansifarverfastmapfontawesomeforcatsfsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGeomxToolsGGallyggbeeswarmggiraphggplot2ggstatsggthemesglobalsgluegtablehighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlme4lmerTestlogNormRegmagrittrMASSMatrixmemoisemgcvmimeminqamunsellNanoStringNCToolsnlmenloptrnortestnumDerivopensslparallellypatchworkpheatmappillarpkgconfigplyrprettyunitsprogressprogressrpurrrR.cacheR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreadxlrematchrepmisreshape2rjsonrlangrmarkdownS4VectorssassscalesSeuratObjectspspamstringistringrsyssystemfontstibbletidyrtidyselecttinytexUCSC.utilsutf8uuidvctrsviporviridisLitewithrxfunXVectoryamlzlibbioc
Use of SpatialDecon in a large GeoMx dataset with GeomxTools
Rendered fromSpatialDecon_vignette_NSCLC.Rmdusingknitr::rmarkdownon Nov 23 2024.Last update: 2023-10-30
Started: 2021-10-13
Use of SpatialDecon in a small GeoMx dataset
Rendered fromSpatialDecon_vignette.Rmdusingknitr::rmarkdownon Nov 23 2024.Last update: 2024-01-11
Started: 2020-07-17
