Package: SiNMFiD 0.0.0.9000

Joshua Sodicoff

SiNMFiD: Supervised iNMF informed Deconvolution

A package for completing cell type deconvolution on bulk spatial transcriptomic data utilizing multiple reference scRNA-seq datasets.

Authors:Joshua Sodicoff [aut, cre], Yichen Wang [ctb]

SiNMFiD_0.0.0.9000.tar.gz
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SiNMFiD.pdf |SiNMFiD.html✨
SiNMFiD/json (API)

# Install 'SiNMFiD' in R:
install.packages('SiNMFiD', repos = c('https://welch-lab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/welch-lab/sinmfid/issues

On CRAN:

2.70 score 1 scripts 30 exports 107 dependencies

Last updated 9 months agofrom:73012e2f3f. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILDec 11 2024
R-4.5-winWARNINGDec 11 2024
R-4.5-linuxWARNINGDec 11 2024
R-4.4-winWARNINGDec 11 2024
R-4.4-macWARNINGDec 11 2024
R-4.3-winWARNINGDec 11 2024
R-4.3-macWARNINGDec 11 2024

Exports:analyze_gene_signaturesanalyze_spatial_correlationcalculate_cell_sizescalculate_wassersteincell_type_loading_histogramdeconvolve_spatialgenerate_label_gifsgenerate_loading_gifslearn_gene_signaturesload_objsmirror_spatial_coordsoverlay_subregion_gifsplot_analyze_gene_signaturesplot_analyze_spatial_correlationplot_calculate_wassersteinplot_summarize_by_layerqc_spatial_datareference_3d_coordinatesregister_voxel_to_labelsample_single_cellsave_spatial_dataselect_defining_genesstart_analysissubset_spatial_datasummarize_by_layersummarize_clusterssummarize_subregionstransform_coords_to_ccfview_in_rglvoxelize_single_cells

Dependencies:base64encBHBiocGenericsbitbit64bslibcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayondata.tabledigestdoParalleldplyrdqrngevaluatefansifarverfastmapFNNfontawesomeforeachfsgenericsGetoptLongggdendroggplot2ggrepelGlobalOptionsgluegridExtragtablehdf5rhighrhtmltoolshtmlwidgetsigraphIRangesirlbaisobanditeratorsjquerylibjsonliteknitrlabelinglatticeleidenAlglifecyclelsamagrittrMASSMatrixmatrixStatsmatrixTestsmemoisemgcvmimemunsellnlmepbmcapplypillarpkgconfigplyrpngpROCR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrglrjsonrlangrligerrmarkdownRSpectraRtsneS4VectorssassscalessccoreshapesitmoSnowballCtibbletidyselecttinytextransportutf8uwotvctrsviridisviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Calculate relationships between cell typesanalyze_gene_signatures
Calculate relationships between cell type distributionsanalyze_spatial_correlation
Calculate cell sizes with all reference datacalculate_cell_sizes
Calculate the Wasserstein distance between cell-types and genescalculate_wasserstein
Generate histograms of loading by cell typecell_type_loading_histogram
Titledeconvolve_spatial
Titlegenerate_label_gifs
Generate gifs of cell type distributions derived from deconvolution in spacegenerate_loading_gifs
Titlelearn_gene_signatures
Load data from one of multiple formatsload_objs
Flip axes in spatial datamirror_spatial_coords
Titleoverlay_subregion_gifs
Plot results of 'analyze_gene_signatures'plot_analyze_gene_signatures
Plot results of 'analyze_spatial_correlation'plot_analyze_spatial_correlation
Plot results of 'calculate_wasserstein'plot_calculate_wasserstein
Plot results of 'summarize_by_layer'plot_summarize_by_layer
Quality-control spatial dataqc_spatial_data
Generate silouhettes of the data along all three axesreference_3d_coordinates
Transfer labels from coarse-grained sampledregister_voxel_to_label
Sample from single cell reference datasetssample_single_cell
Add a new spatial dataset to the analysis directorysave_spatial_data
select variable genes with the Kruskal-Wallis testselect_defining_genes
Set up new analysis directorystart_analysis
Subset a spatial dataset by coordinates for analysissubset_spatial_data
Summarize cell-type and gene expression data bysummarize_by_layer
Summarize cell types present in the source annotationssummarize_clusters
Summarize subregions of a vector of regions of interestsummarize_subregions
Use predefined transformations to match some modalities to the Allen CCFtransform_coords_to_ccf
Titleview_in_rgl
Coarse-grain spatial data to a predetermined resolutionvoxelize_single_cells