Files in CamaraLab/STvEA
Spatially-resolved Transcriptomics via Epitope Anchoring

.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/STvEA-package.R R/clustering.R R/data_processing.R R/feature_scores.R R/mapping.R R/objects.R R/plotting.R R/seurat_anchor_correction.R README.md
data/MGL02_Spleen_Live_cells.fcs
data/codex_balbc1.RData
examples/codex_tutorial.Rmd examples/codex_tutorial.md
examples/codex_tutorial_files/figure-markdown_github/unnamed-chunk-10-1.png
examples/codex_tutorial_files/figure-markdown_github/unnamed-chunk-11-1.png
examples/codex_tutorial_files/figure-markdown_github/unnamed-chunk-12-1.png
examples/codex_tutorial_files/figure-markdown_github/unnamed-chunk-13-1.png
examples/codex_tutorial_files/figure-markdown_github/unnamed-chunk-14-1.png
examples/codex_tutorial_files/figure-markdown_github/unnamed-chunk-15-1.png
examples/codex_tutorial_files/figure-markdown_github/unnamed-chunk-16-1.png
examples/cytof_tutorial.Rmd examples/cytof_tutorial.md
examples/cytof_tutorial_files/figure-markdown_github/unnamed-chunk-7-1.png
examples/cytof_tutorial_files/figure-markdown_github/unnamed-chunk-8-1.png
examples/cytof_tutorial_files/figure-markdown_github/unnamed-chunk-9-1.png
examples/mapping_tutorial.Rmd examples/mapping_tutorial.md
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-11-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-17-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-18-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-19-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-20-1.png
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examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-23-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-24-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-25-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-26-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-27-1.png
examples/mapping_tutorial_files/figure-markdown_github/unnamed-chunk-28-1.png
examples/seurat_tutorial.Rmd examples/seurat_tutorial.md
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-14-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-15-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-16-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-17-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-18-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-19-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-20-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-21-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-22-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-23-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-24-1.png
examples/seurat_tutorial_files/figure-markdown_github/unnamed-chunk-25-1.png
inst/python/consensus_clustering.py
man/AdjScoreClustersCITE.Rd man/AdjScoreClustersCITE.internal.Rd man/AdjScoreClustersCODEX.Rd man/AdjScoreClustersCODEX.internal.Rd man/AdjScoreGenes.Rd man/AdjScoreGenes.internal.Rd man/AdjScoreHeatmap.Rd man/AdjScoreProteins.Rd man/AdjScoreProteins.internal.Rd man/AnchorCorrection.Rd man/CleanCITE.Rd man/CleanCITE.gaussian.internal.Rd man/CleanCITE.nb.internal.Rd man/CleanCODEX.Rd man/CleanCODEX.gaussian.internal.Rd man/CleanCODEX.nb.internal.Rd man/ClusterCODEX.Rd man/ClusterCODEX.internal.Rd man/ConsensusCluster.Rd man/ConsensusCluster.internal.Rd man/ConstructNNMat.Rd man/CorNN.Rd man/FilterAnchors.Rd man/FilterCITEmRNA.Rd man/FilterCITEmRNA.internal.Rd man/FilterCODEX.Rd man/FilterCODEX.internal.Rd man/FindAnchorPairs.Rd man/FindIntegrationMatrix.Rd man/FindNN.Rd man/FindNNrna.Rd man/FindWeights.Rd man/FitGaussian.Rd man/FitNB.Rd man/GetTransferMatrix.Rd man/GetTransferMatrix.internal.Rd man/GetUmapCITE.Rd man/GetUmapCODEX.Rd man/KnnCODEX.Rd man/L2Norm.Rd man/MapCODEXtoCITE.Rd man/MapCODEXtoCITE.internal.Rd man/NormCells.Rd man/ParameterScan.Rd man/ParameterScan.internal.Rd man/PlotClusterCITE.Rd man/PlotClusterCODEXemb.Rd man/PlotExprCITE.Rd man/PlotExprCODEXemb.Rd man/PlotExprCODEXspatial.Rd man/PlotIndexCITE.Rd man/PlotIndexCODEXemb.Rd man/PlotIndexCODEXspatial.Rd man/ReadDataFCS.Rd man/ReadNamesFCS.Rd man/RunCCA.Rd man/SSE.Rd man/STvEA-package.Rd man/STvEA.data-class.Rd man/ScoreAnchors.Rd man/SetDataCITE.Rd man/SetDataCODEX.Rd man/TransferDataSeurat2.Rd man/TransformDataMatrix.Rd man/clustering_names.Rd man/hello.Rd
shinyapp/#app.R#
shinyapp/CODEX_BALBc-1_filtered_spatial.txt
shinyapp/CODEX_BALBc-2_filtered_spatial.txt
shinyapp/CODEX_BALBc-3_filtered_spatial.txt
shinyapp/app.R
shinyapp/app.R~
shinyapp/application.yml~
shinyapp/cite_gene.rds
shinyapp/cite_nn_exp_BALBc-1.rds
shinyapp/cite_nn_exp_BALBc-2.rds
shinyapp/cite_nn_exp_BALBc-3.rds
shinyapp/cluster_labels.csv
shinyapp/codex_exp_clean_BALBc1.rds
shinyapp/codex_exp_clean_BALBc2.rds
shinyapp/codex_exp_clean_BALBc3.rds
shinyapp/data.R
shinyapp/data.R~
shinyapp/filtered_gene_matrix_combined_uncut.rds
shinyapp/genes.tsv
shinyapp/protein_expr_corrected_clean.csv
shinyapp/rsconnect/shinyapps.io/camara-lab/stvea.dcf
shinyapp/server.R shinyapp/ui.R
shinyapp/ui.R~
shinyapp/umap_embedding_combined_nocycle.csv
shinyapp/umap_embedding_v2.csv
shinyapp/www/C57BL.png
shinyapp/www/C57BL.svg
shinyapp/www/ace-1.png
shinyapp/www/ace-1.svg
shinyapp/www/ace-cd3-1.png
shinyapp/www/ace-cd3-1.svg
shinyapp/www/clusters.svg
shinyapp/www/codex-mouse1.png
shinyapp/www/codex-mouse2.png
shinyapp/www/codex-mouse3.png
shinyapp/www/outline.svg
CamaraLab/STvEA documentation built on March 27, 2024, 8:58 a.m.