Files in supatt-lab/SingCellaR
SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/Import.R
R/RcppExports.R
R/SingleCellClasses.R
R/SingleCellGenerics.R
R/SingleCellPlots.R
R/SingleCellRNASeq.R
R/SingleCellUtils.R
R/SingleCell_Integration.R
R/zzz.R
README.md
SingCellaR.Rproj
man/Build_AUCell_Rankings.Rd
man/Build_AUCell_Rankings_Fast.Rd
man/DoubletDetection_with_scrublet.Rd
man/Run_AUCell.Rd
man/Run_fGSEA_analysis.Rd
man/Run_fGSEA_for_a_selected_cluster_vs_the_rest_of_clusters.Rd
man/Run_fGSEA_for_multiple_comparisons.Rd
man/SingCellaR.Rd
man/TargetSeq_filter_cells_and_genes.Rd
man/TargetSeq_load_cell_metadata.Rd
man/TargetSeq_plot_cells_annotation.Rd
man/TargetSeq_process_cells_annotation.Rd
man/add_cell_cycle_genes_score.Rd
man/clustering_KMeansOnKNN_Graph.Rd
man/export_marker_genes_to_table.Rd
man/filter_cells_and_genes.Rd
man/findMarkerGenes.Rd
man/getCellsFromClusters.Rd
man/getMarkerGenesInfo.Rd
man/get_cells_annotation.Rd
man/get_clusters.Rd
man/get_dfm.result.Rd
man/get_dir_path_10x_matrix.Rd
man/get_fa2_graph.layout.Rd
man/get_genes_metadata.Rd
man/get_gmtGeneSets.Rd
man/get_knn_graph.graph.Rd
man/get_knn_graph.layout.Rd
man/get_lsi.result.Rd
man/get_marker_genes.Rd
man/get_nnmf.result.Rd
man/get_normalized_umi.Rd
man/get_pca.result.Rd
man/get_regressout_log_data.Rd
man/get_sample_uniq_id.Rd
man/get_tsne.result.Rd
man/get_umap.result.Rd
man/get_umi_count.Rd
man/get_variable_genes_basic.Rd
man/get_variable_genes_by_fitting_GLM_model.Rd
man/get_variable_genes_for_integrative_data_by_fitting_GLM_model.Rd
man/identifyClusters.Rd
man/identifyDifferentialGenes.Rd
man/identifyDifferentialGenes_for_all_clusters.Rd
man/identifyDifferentialGenes_in_a_cluster_vs_the_rest_of_clusters.Rd
man/identifyDifferentialGenes_in_multiple_clusters_vs_the_rest_of_clusters.Rd
man/identifyGSEAPrerankedGenes.Rd
man/identifyGSEAPrerankedGenes_for_all_clusters.Rd
man/identifyGSEAPrerankedGenes_in_a_cluster_vs_the_rest_of_clusters.Rd
man/identify_potentially_merging_clusters.Rd
man/listAvailableGeneSets.Rd
man/load_gene_expression_from_a_file.Rd
man/load_matrices_from_cellranger.Rd
man/merge_clusters.Rd
man/normalize_UMIs.Rd
man/plot_3D_knn_graph_label_by_a_signature_gene_set.Rd
man/plot_3D_knn_graph_label_by_clusters.Rd
man/plot_3D_knn_graph_label_by_gene.Rd
man/plot_PCA_Elbowplot.Rd
man/plot_ShortestPath_on_3D_knn_graph.Rd
man/plot_ShortestPath_on_forceDirectedGraph_label_by_clusters.Rd
man/plot_UMIs_of_HouseKeepingGenes.Rd
man/plot_UMIs_vs_Detected_genes.Rd
man/plot_bubble_for_genes_per_cluster.Rd
man/plot_bubble_for_genes_per_custom_group_of_cells.Rd
man/plot_cells_annotation.Rd
man/plot_diffusionmap_label_by_clusters.Rd
man/plot_diffusionmap_label_by_genes.Rd
man/plot_diffusionmap_label_by_multiple_gene_sets.Rd
man/plot_forceDirectedGraph_label_by_AUCell_score.Rd
man/plot_forceDirectedGraph_label_by_a_feature_of_interest.Rd
man/plot_forceDirectedGraph_label_by_a_signature_gene_set.Rd
man/plot_forceDirectedGraph_label_by_clusters.Rd
man/plot_forceDirectedGraph_label_by_genes.Rd
man/plot_forceDirectedGraph_label_by_multiple_gene_sets.Rd
man/plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited_sampleID.Rd
man/plot_forceDirectedGraph_label_by_qc.Rd
man/plot_forceDirectedGraph_label_by_sampleID.Rd
man/plot_forceDirectedGraph_label_by_selected_sampleID.Rd
man/plot_heatmap_for_differential_genes.Rd
man/plot_heatmap_for_fGSEA_all_clusters.Rd
man/plot_heatmap_for_marker_genes.Rd
man/plot_jaccard_similarity_among_clusters.Rd
man/plot_tsne_label_by_AUCell_score.Rd
man/plot_tsne_label_by_a_feature_of_interest.Rd
man/plot_tsne_label_by_a_signature_gene_set.Rd
man/plot_tsne_label_by_clusters.Rd
man/plot_tsne_label_by_genes.Rd
man/plot_tsne_label_by_multiple_gene_sets.Rd
man/plot_tsne_label_by_multiple_gene_sets_with_limited_sampleID.Rd
man/plot_tsne_label_by_qc.Rd
man/plot_tsne_label_by_sampleID.Rd
man/plot_tsne_label_by_selected_sampleID.Rd
man/plot_umap_label_by_AUCell_score.Rd
man/plot_umap_label_by_a_feature_of_interest.Rd
man/plot_umap_label_by_a_signature_gene_set.Rd
man/plot_umap_label_by_clusters.Rd
man/plot_umap_label_by_genes.Rd
man/plot_umap_label_by_multiple_gene_sets.Rd
man/plot_umap_label_by_multiple_gene_sets_with_limited_sampleID.Rd
man/plot_umap_label_by_qc.Rd
man/plot_umap_label_by_sampleID.Rd
man/plot_umap_label_by_selected_sampleID.Rd
man/plot_variable_genes.Rd
man/plot_violin_for_differential_genes.Rd
man/plot_violin_for_genes_per_custom_group_of_cells.Rd
man/plot_violin_for_marker_genes.Rd
man/preprocess_integration.Rd
man/preprocess_integration_for_ADT.Rd
man/process_cells_annotation.Rd
man/remove_clusters.Rd
man/remove_unwanted_confounders.Rd
man/remove_unwanted_genes_from_variable_gene_set.Rd
man/runCombat.Rd
man/runDiffusionMap.Rd
man/runFA2_ForceDirectedGraph.Rd
man/runHarmony.Rd
man/runKBET.Rd
man/runKNN_Graph.Rd
man/runLISI.Rd
man/runLiger_online_iNMF.Rd
man/runNNMF.Rd
man/runPCA.Rd
man/runScanorama.Rd
man/runSeuratIntegration.Rd
man/runSeuratIntegration_with_rpca.Rd
man/runSupervised_Harmony.Rd
man/runTSNE.Rd
man/runUMAP.Rd
man/show-methods.Rd
man/sub_clusters.Rd
man/subsample_cells.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/RcppExports.o
src/RcppPerpendicular.h
src/SingCellaR.so
src/matrix.h
src/nn_parallel.h
src/utils.cpp
src/utils.o
