Man pages for AlexanderKononov/cytofCore
Detail analysis and visualisation CyTOF data
| abundence_meter | Low-level function to calculate abundances for each cluster... |
| add_cluster_GDB | Add clusters as nodes to neo4j database |
| add_marker_GDB | Add markers as nodes to neo4j database |
| add_observation_GDB | Allocate observations as nodes based on marker and cell... |
| add_phenounite_GDB | Allocate phenounite, phenotype units, nodes based on markers... |
| add_populatio_GDB | Allocate cell populations within each sample based on... |
| add_sample_GDB | Add samples as nodes to neo4j database |
| add_signals_between_clusters_GDB | Add correlation between clusters as relationships to the... |
| add_signals_in_cluster_GDB | Add correlation within clusters as relationships to the... |
| asinh_transformation | Transformation from "count" to "asinh" data |
| backgraund_correlation | Get bg_ctCor_data object with background correlation... |
| background_anova | Get bg_anova object with background ANOVA statistics |
| cell_filter | Low-level function for comparison of detected correlations... |
| cell_type_organiser | Low-level function to get cell_ctDist object for one sample |
| cluster_merging | Merging two or more clusters within cluster annotating vector |
| cluster_unification | Low-level function for unification of clusters set between... |
| comparator_mk | Compare background correlation landscape versus target... |
| ct_sample_aggregator | Get list_cell_ctDist object for correlation analysis |
| cytofBrowserGUI | The main function to run cutofCore graphic interface |
| cytofBrowser_server | Creation of server part of Shiny App |
| filter_edges | Filter out edges which have weight more than threshold |
| filter_mk | Filtering signals by background comparison information |
| get_abundance | Get data of cluster abundace |
| get_abundance_correlation | Calculation of correlation between cluster by abundance data |
| get_abundance_dataframe | Create the data table to draw the abundance barplot |
| get_abund_cross_panel | Compiling the matrix with cluster abundance data for all... |
| get_add_cell_annotation_from_data | Extract annotation fron fcs_raw object to cell annotation... |
| get_adj_corr_pValue_matrix | Extraction adjusted p-value from abundance correlation data |
| get_anova_mk | Get anova_mk object with ANOVA statistics for markers within... |
| get_bg_anova_land_mk | Get bg_anova_land_mk object with background ANOVA statistics... |
| get_bg_corr_land_mk | Calculate background correlation landscape between markers... |
| get_bg_naive_corr_land_mk | Background correlation landscape between markers |
| get_cell_annotation_fcs_files | Adding of cluster-info to flowSet object |
| get_cell_clustering_vector | Create the cluster annotation as one vector |
| get_cell_number | Extract cell number |
| get_cell_type_from_gates | Function adds set of gates to cell annotation object |
| get_cluster_annotation | Create the cluster annotation separated by samples |
| get_clustered_fcs_files | Adding of cluster-info to flowSet object |
| get_clustering_exp_cell_f_cross_panel | Get dxpressing cell fraction data for target marker |
| get_common_markers | Extracting of common markers across panels and formed a... |
| get_consensusClust | Get mc consensusCluster object from ConsensusClusterPlus |
| get_contrast_corr_land_mk | Contrast correlation landscape |
| get_contrast_naive_corr_land_mk | Get contrast naive correlation landscape for each clone each... |
| get_corr_coef_matrix | Extraction correlation coefficient from abundance correlation... |
| get_corr_pValue_matrix | Extraction p-value from abundance correlation data |
| get_data_for_gating | Take data to gating scatterplot |
| get_deconvol_dataframe | Get dataframe for deconvolution plot of markers to... |
| get_edges | Get edges |
| get_entire_panel | Create entire named vector with obsermations:... |
| get_euclid_dist | Get euclidean distance between clones |
| get_fcs_cell_clustering_vector | Create the cluster annotation as one vector for cluster info... |
| get_fcs_cluster_annotation | Create the cluster annotation separated by samples from fcs... |
| get_fcs_metadata | Create basic metadata for flowSet object |
| get_fcs_panel | Create panel data to fowSet object |
| get_fcs_raw | Creat FlowSet object |
| get_inds_subset | Get indexs of rows with were sampled to subset |
| get_list_cell_ctDist | Get list_cell_ctDist object to correlation analysis |
| get_list_expData | Get list_expData object to correlation analysis |
| get_matrices_corr_info | Produce three matrices with corr coefficient, p-value and... |
| get_mk_clust_heatmap_dataframe | Get dataframe for marker-cluster heatmap |
| get_neo_api | Create api for neo4j session |
| get_nodes | Get nodes |
| get_optimal_clusters | Get a optimal number of clusters |
| get_panel_content | Matrix for plotting the content of panels |
| get_signal_between_cluster_mk | Extract signals which go from one cluster and go to another |
| get_signal_in_cluster_mk | Extract signals which go from and to the same cluster |
| get_signals_between_clusters | Convert from signal dataframe to tidy dataframe with... |
| get_signals_between_clusters_top | Get the top of significant signals from... |
| get_signals_in_cluster | Convert from signal dataframe to tidy dataframe with... |
| get_signals_in_cluster_top | Get the top of significant signals from... |
| get_som | Get som object from flowSOM |
| get_test_fcs_metadata | extract metadata for build-in test dataset |
| get_threshold_exp_cell_f_cross_panel | Extract expression data of one marker for coss-panel analysis... |
| get_UMAP_dataframe | Title |
| get_use_marker | filtering out technical markers |
| get_write_corr_info_cross_p | Preparing the table with cross-panel correlations for... |
| htest_data_extractor | Low-level function for correlation analysis of genes from all... |
| htest_data_extractor_mk | Correlation analysis between markers of different clusters |
| neo_api_ping | Checking connection to neo4j |
| outlier_by_quantile_transformation | Transformation to a from 0 to 1 variable and removing... |
| scatter_plot_data_prep | Preparing data to tSNE |
| signal_extractor | Get signal_Stat object with complete signal information from... |
| signal_filter | The first function for filtration of signals |
| take_top_correlation | Low-level function for extraction of top significant... |
| target_type_cortest | Low-level function for correlation analysis of genes from one... |
| target_type_data_extractor | Low-level function to format detected signals to result... |
| target_type_organiser | Low-level function to get tt_expData object for one sample |
| tt_sample_aggregator | Get list_tt_expData object for correlation analysis |
