Package: ProFAST 1.4

Wei Liu

ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations. More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.

Authors:Wei Liu [aut, cre], Xiao Zhang [aut], Jin Liu [aut]

ProFAST_1.4.tar.gz
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ProFAST.pdf |ProFAST.html✨
ProFAST/json (API)

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

Peer review:

Bug tracker:https://github.com/feiyoung/profast/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • CosMx_subset - A Seurat object including spatial transcriptomics dataset from CosMx platform
  • pbmc3k_subset - A Seurat object including scRNA-seq PBMC dataset
  • top5_signatures - A data.frame object including top five signature genes in scRNA-seq PBMC dataset

On CRAN:

22 exports 2 stars 1.18 score 239 dependencies 10 scripts 176 downloads

Last updated 6 months agofrom:66d59e1ec9. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-win-x86_64NOTEAug 27 2024
R-4.5-linux-x86_64NOTEAug 27 2024
R-4.4-win-x86_64NOTEAug 27 2024
R-4.4-mac-aarch64NOTEAug 27 2024
R-4.4-mac-x86_64NOTEJul 28 2024
R-4.3-win-x86_64NOTEAug 27 2024
R-4.3-mac-x86_64NOTEAug 27 2024
R-4.3-mac-aarch64NOTEAug 27 2024

Exports:AddAdjAddParSettingFASTcoembed_plotcoembedding_umapdiagnostic.cor.eigsFASTFAST_runFAST_singleFAST_structurefind.signature.genesget_r2_mcfaddenget.top.signature.datIntegrateSRTDataiscmeb_runmodel_set_FASTNCFMNCFM_fastpdistanceRunHarmonyLouvainRuniSCMEBSelectHKgenestransferGeneNames

Dependencies:abindAnnotationDbiaskpassbackportsbase64encbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularbiomaRtBiostringsbitbit64bitopsblobbootbroombslibcachemCairocarcarDatacaToolscliclustercodetoolscolorspacecommonmarkCompQuadFormcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirDerivdigestdoBydotCall64dplyrdqrngDR.SCevaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomeformatRfsfurrrfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggpubrggrastrggrepelggridgesggsciggsignifggthemesGiRaFglobalsgluegoftestgplotsgridExtragtablegtoolsharmonyherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemgcvmicrobenchmarkmimeminiUIminqamodelrmunsellnlmenloptrnnetnumDerivopensslorg.Hs.eg.dborg.Mm.eg.dbparallellypatchworkpbapplypbkrtestpheatmappillarpkgconfigplogrplotlyplyrpngpolyclippolynomPRECASTprettyunitsprogressprogressrpromisespurrrquantregR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulateRhpcBLASctlrlangrmarkdownROCRrprojrootRSpectraRSQLiterstatixrsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraySparseMspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunxml2xtableXVectoryamlzlibbioczoo

CoFAST: NSCLC CosMx data coembedding

Wei Liu

Rendered fromCosMx.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2024-03-16
Started: 2024-03-16

CoFAST: PBMC scRNA-seq data coembedding

Wei Liu

Rendered frompbmc3k.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2024-03-18
Started: 2024-03-16

FAST: simulation

Wei Liu

Rendered fromFASTsimu.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2024-01-11
Started: 2024-01-11

FAST: single DLPFC section

Wei Liu

Rendered fromFASTdlpfc.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2024-03-17
Started: 2024-03-16

FAST: two DLPFC sections

Wei Liu

Rendered fromFASTdlpfc2.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2024-03-16
Started: 2024-01-11

Readme and manuals

Help Manual

Help pageTopics
Calculate the adjacency matrix given a spatial coordinate matrixAddAdj
Add FAST model settings for a PRECASTObj objectAddParSettingFAST
Coembedding dimensional reduction plotcoembed_plot
Calculate UMAP projections for coembedding of cells and featurescoembedding_umap
A Seurat object including spatial transcriptomics dataset from CosMx platformCosMx_subset
Determine the dimension of low dimensional embeddingdiagnostic.cor.eigs diagnostic.cor.eigs.default diagnostic.cor.eigs.Seurat
Run FAST model for a PRECASTObj objectFAST
(Varitional) ICM-EM algorithm for implementing FAST modelFAST_run
Fit FAST model for single-section SRT dataFAST_single
(Varitional) ICM-EM algorithm for implementing FAST model with structurized parametersFAST_structure
Find the signature genes for each group of cell/spotsfind.signature.genes
Calcuate the the adjusted McFadden's pseudo R-squareget_r2_mcfadden
Obtain the top signature genes and related informationget.top.signature.dat
Integrate multiple SRT data into a Seurat objectIntegrateSRTData
Fit an iSC-MEB model using specified multi-section embeddingsiscmeb_run
Set parameters for FAST modelmodel_set_FAST
Cell-feature coembedding for scRNA-seq dataNCFM
Cell-feature coembedding for SRT dataNCFM_fast
A Seurat object including scRNA-seq PBMC datasetpbmc3k_subset
Calculate the cell-feature distance matrixpdistance
Embedding alignment and clustering based on the embeddings from FASTRunHarmonyLouvain
Fit an iSC-MEB model using the embeddings from FASTRuniSCMEB
Select housekeeping genesSelectHKgenes
A data.frame object including top five signature genes in scRNA-seq PBMC datasettop5_signatures
Transfer gene names from one fortmat to the other formattransferGeneNames