API for hms-dbmi/drugseqr
GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations
| Global functions | |
|---|---|
| NNTransform | Source code |
| SingleViolinIPlot | Man page Source code |
| actionGroupButtonsWithClickHandlers | Source code |
| add_adjusted | Source code |
| add_alpha | Source code |
| add_cluster_numbers | Man page Source code |
| add_combined_ambience | Source code |
| add_combined_metrics | Man page Source code |
| add_doublet_score | Man page Source code |
| add_grid_colors | Source code |
| add_hvgs | Man page Source code |
| add_linkout | Man page |
| add_optgroup_type | Source code |
| add_scseq_qc_metrics | Man page Source code |
| add_scseq_qcplot_metrics | Man page Source code |
| add_table_html | Man page |
| add_vsd | Source code |
| advancedOptions | Source code |
| advancedOptionsInput | Man page Source code |
| aggregate.Matrix | Man page Source code |
| aggregate_across_cells | Source code |
| annot_query_res | Man page Source code |
| append_annot | Man page |
| attach_clusters | Source code |
| attach_meta | Source code |
| attrib_replace | Source code |
| boxPlotly | Man page Source code |
| boxPlotlyCells | Man page Source code |
| bulkAnal | Source code |
| bulkAnalInput | Source code |
| bulkAnnot | Source code |
| bulkAnnotInput | Source code |
| bulkCellsPlotly | Source code |
| bulkDataset | Source code |
| bulkDatasetInput | Source code |
| bulkExploreTable | Source code |
| bulkForm | Source code |
| bulkFormAnal | Source code |
| bulkFormAnalInput | Source code |
| bulkFormInput | Source code |
| bulkGenePlotly | Source code |
| bulkMDS | Source code |
| bulkMDSplotly | Source code |
| bulkPage | Man page Source code |
| bulkPageUI | Man page Source code |
| bulkPlotlyUI | Source code |
| bulkTable | Source code |
| calc_deconv_hash | Source code |
| calculate_cluster_ambience | Source code |
| calcx | Man page |
| cbind.safe | Source code |
| check_bulk_changed | Man page Source code |
| check_gras | Man page Source code |
| check_has_scseq | Man page Source code |
| check_is_market_matrix | Man page Source code |
| clean_kb_scseq | Man page Source code |
| clusterComparison | Source code |
| clusterComparisonInput | Source code |
| clustersMergeForm | Source code |
| col2hex | Source code |
| collapse_sorted | Man page Source code |
| comparisonType | Source code |
| comparisonTypeToggle | Source code |
| confirmImportBulkModal | Source code |
| confirmImportSingleCellModal | Source code |
| confirmMergeModal | Source code |
| confirmSubsetModal | Source code |
| construct_path_df | Man page Source code |
| construct_pbulk_subsets | Man page Source code |
| construct_top_markers | Source code |
| convert_species | Source code |
| create_scseq | Man page Source code |
| customQueryForm | Source code |
| customQueryFormInput | Man page Source code |
| dMcast | Source code |
| datasets_to_list | Man page Source code |
| deconvForm | Source code |
| deconvFormInput | Source code |
| deconv_bulk_dtangle | Source code |
| deconv_bulk_dwls | Source code |
| deconv_bulk_music | Source code |
| deleteModal | Source code |
| detect_10x_chemistry | Man page Source code |
| detect_cells | Man page Source code |
| detect_import_species | Source code |
| diff_abundance | Man page Source code |
| dir_exists | Man page Source code |
| disableAll | Man page Source code |
| disableMobileKeyboard | Source code |
| dl_pert_result | Man page Source code |
| dl_pert_signature | Man page Source code |
| downloadResultsModal | Source code |
| download_kb_index | Man page Source code |
| downsample_clusters | Man page Source code |
| dropdownButtonMod | Man page Source code |
| dropdownMenuButton | Man page Source code |
| drugsForm | Source code |
| drugsFormInput | Man page Source code |
| drugsGenesPlotly | Source code |
| drugsGenesPlotlyOutput | Man page Source code |
| drugsPage | Man page Source code |
| drugsPageUI | Man page Source code |
| drugsTable | Source code |
| drugsTableOutput | Man page Source code |
| dsLabelRowsUI | Source code |
| enableAll | Man page Source code |
| es_to_tt | Source code |
| evaluate_custom_metric | Man page Source code |
| exploreEset | Source code |
| exportModal | Source code |
| extract_enids | Source code |
| file.move | Source code |
| file_exists | Man page Source code |
| filter_clinical | Man page Source code |
| filter_nsig | Man page Source code |
| find_merged_clusters | Source code |
| find_robject | Source code |
| fit_lm | Source code |
| format_comma_regex | Source code |
| format_dl_annot | Man page Source code |
| format_markers_for_dwls | Source code |
| format_query_res | Man page Source code |
| format_scaling | Source code |
| format_up_annot | Man page Source code |
| format_up_custom | Man page Source code |
| from_crossmeta | Man page Source code |
| getDeleteRowButtons | Man page Source code |
| getUploadBulkInfo | Source code |
| get_ambience | Man page Source code |
| get_boxplotly_cell_args | Man page Source code |
| get_boxplotly_gene_args | Man page Source code |
| get_cell_choices | Man page Source code |
| get_celldex_species | Source code |
| get_cluster_choices | Man page Source code |
| get_cluster_markers | Man page Source code |
| get_cluster_stats | Man page Source code |
| get_clusters | Source code |
| get_contrast_choices | Man page Source code |
| get_contrast_markers | Man page Source code |
| get_cors_html | Man page |
| get_dist | Man page Source code |
| get_dprimes | Man page Source code |
| get_drug_paths | Man page Source code |
| get_drugbank | Man page Source code |
| get_drugs_table | Man page Source code |
| get_dtangle_pvals | Source code |
| get_exclude_cells | Source code |
| get_expression_colors | Man page Source code |
| get_founder | Man page Source code |
| get_gene_table | Source code |
| get_genego | Man page Source code |
| get_gonames | Man page Source code |
| get_grid | Source code |
| get_grid_abundance | Source code |
| get_grid_expression | Source code |
| get_grid_size | Source code |
| get_group_levels | Man page Source code |
| get_html_features | Source code |
| get_integrated_datasets | Source code |
| get_integration_species | Source code |
| get_kb_version | Source code |
| get_label_coords | Source code |
| get_label_transfer_choices | Man page Source code |
| get_leftover_table | Source code |
| get_mds | Man page Source code |
| get_metric_choices | Man page Source code |
| get_metric_features | Man page Source code |
| get_nearest_row | Man page Source code |
| get_need_multisample | Source code |
| get_npc_choices | Man page Source code |
| get_open_a | Man page |
| get_paired_pval | Source code |
| get_palette | Man page Source code |
| get_path_df | Man page Source code |
| get_path_res | Man page Source code |
| get_pred_annot | Man page Source code |
| get_presto_markers | Man page Source code |
| get_qc_table | Source code |
| get_query_cols | Man page Source code |
| get_ref_cols | Source code |
| get_ref_resoln | Source code |
| get_ref_type | Source code |
| get_refs_list | Source code |
| get_resoln_dir | Source code |
| get_resoln_name | Man page Source code |
| get_sc_dataset_choices | Man page Source code |
| get_scatter_props | Source code |
| get_scdata_type | Source code |
| get_selected_from_transfer_name | Source code |
| get_snn_graph | Source code |
| get_species | Man page Source code |
| get_species_choices | Source code |
| get_top | Man page Source code |
| get_top_cors | Man page |
| get_tsne_coords | Man page Source code |
| get_unpaired_pval | Source code |
| get_violin_data | Man page Source code |
| get_wikipedia | Man page Source code |
| group_terms | Source code |
| handle_bulk_progress | Source code |
| handle_sc_progress | Man page Source code |
| hash_meta | Source code |
| html_space | Man page Source code |
| id_from_tab | Man page Source code |
| identify_sc_files | Man page Source code |
| importSingleCellModal | Source code |
| import_robject | Source code |
| import_scseq | Man page Source code |
| index_last | Source code |
| init_dseqr | Man page Source code |
| integrate_saved_scseqs | Man page Source code |
| integrate_scseqs | Man page Source code |
| integrationForm | Source code |
| integrationModal | Source code |
| interpret | Man page Source code |
| iqr_replicates | Source code |
| is.numstring | Source code |
| isTruthy | Man page Source code |
| isTruthyAll | Man page Source code |
| is_invertible | Man page Source code |
| justifiedButtonGroup | Man page Source code |
| keep_curr_selected | Man page Source code |
| knn_predict | Source code |
| labelTransferForm | Source code |
| labelTransferFormInput | Source code |
| limit_cells | Man page Source code |
| load_args | Source code |
| load_bulk_datasets | Man page Source code |
| load_cellranger_counts | Man page Source code |
| load_cellranger_genes | Source code |
| load_custom_anals | Man page Source code |
| load_custom_results | Man page Source code |
| load_drug_es | Man page Source code |
| load_kallisto_counts | Man page Source code |
| load_pert_anals | Man page Source code |
| load_pert_signature | Man page Source code |
| load_resoln | Man page Source code |
| load_scseq_datasets | Man page Source code |
| load_scseq_qcgenes | Man page Source code |
| load_scseq_qs | Man page Source code |
| load_scseq_subsets | Man page Source code |
| load_tx2gene | Source code |
| make_unique | Man page Source code |
| mergeClustersInput | Source code |
| merge_clusters | Source code |
| merge_linkouts | Man page |
| merge_samples | Man page Source code |
| name_list | Source code |
| navbar2UI | Man page Source code |
| navbarUI | Man page Source code |
| normalize_eset | Source code |
| normalize_scseq | Man page Source code |
| plot_biogps | Man page Source code |
| plot_dprimes | Man page |
| plot_violin | Man page Source code |
| plotlyMDS | Man page Source code |
| prep_scseq_export | Source code |
| pretty.unique | Source code |
| process_cellranger_counts | Source code |
| process_raw_scseq | Man page Source code |
| process_robject_multisample | Source code |
| process_robject_samples | Source code |
| qread.safe | Man page Source code |
| query_budger | Man page Source code |
| query_drugs | Man page Source code |
| range02 | Source code |
| remove.unique | Source code |
| remove_dataset_files | Man page Source code |
| req | Man page Source code |
| resolutionForm | Source code |
| resolutionFormInput | Source code |
| rightClickMenu | Man page Source code |
| run_azimuth | Source code |
| run_azimuth_sample | Source code |
| run_custom_query | Man page Source code |
| run_drug_queries | Man page Source code |
| run_dseqr | Man page Source code |
| run_dseqr_shinyproxy | Source code |
| run_esmeta | Source code |
| run_esmeta_logc | Source code |
| run_fastmnn | Man page Source code |
| run_go | Source code |
| run_harmony | Man page Source code |
| run_import_scseq | Source code |
| run_integrate_saved_scseqs | Man page Source code |
| run_kallisto_bulk_bg | Source code |
| run_kb_count | Source code |
| run_kb_scseq | Man page Source code |
| run_label_transfer | Source code |
| run_limma_scseq | Man page Source code |
| run_pca | Man page Source code |
| run_pmeta | Source code |
| run_post_cluster | Man page Source code |
| run_reduction | Man page Source code |
| run_scseq_qc | Man page Source code |
| run_symphony | Source code |
| safe.fun | Source code |
| safe_set_annot | Source code |
| safe_set_clusters | Source code |
| safe_set_meta | Source code |
| sammon | Source code |
| save_lmfit | Man page Source code |
| save_ref_clusters | Source code |
| save_scseq_args | Man page Source code |
| save_scseq_data | Man page Source code |
| save_split_mtxs | Source code |
| scAbundancePlotOutput | Source code |
| scBioGpsPlot | Source code |
| scBioGpsPlotOutput | Source code |
| scClusterPlot | Source code |
| scClusterPlotOutput | Source code |
| scForm | Source code |
| scFormInput | Source code |
| scGridAbundance | Source code |
| scMarkerPlot | Source code |
| scMarkerPlotOutput | Source code |
| scPage | Man page Source code |
| scPageUI | Man page Source code |
| scSampleClusters | Source code |
| scSampleClustersInput | Source code |
| scSampleGroups | Source code |
| scSampleGroupsInput | Source code |
| scSamplePlot | Source code |
| scSamplePlotOutput | Source code |
| scSelectedDataset | Source code |
| scSelectedDatasetInput | Source code |
| scViolinPlot | Source code |
| scViolinPlotOutput | Source code |
| sc_dl_filename | Man page Source code |
| scseq_part_path | Man page Source code |
| selectedAnal | Source code |
| selectedAnalInput | Man page Source code |
| selectedDrugStudy | Source code |
| selectedDrugStudyInput | Man page Source code |
| selectedGene | Source code |
| selectedGeneInput | Source code |
| selectedPertSignature | Source code |
| selectedPertSignatureInput | Man page Source code |
| send_slack_error | Man page Source code |
| seurat_to_sce | Source code |
| shorten_y | Source code |
| simplify | Source code |
| slackify_stack | Source code |
| sort_clusters | Man page Source code |
| sort_query_table_clin | Man page |
| species_symbols_to_other | Source code |
| split_mtx | Source code |
| split_save_scseq | Source code |
| split_scseq | Source code |
| standardize_cellranger | Man page Source code |
| subsetForm | Source code |
| subsetFormInput | Source code |
| subset_contrast | Source code |
| subset_saved_scseq | Man page Source code |
| summarise_query_table | Man page Source code |
| summarize_compound | Man page Source code |
| svaButton | Source code |
| tabPane | Man page Source code |
| theme_dimgray | Man page Source code |
| theme_no_axis_vals | Source code |
| theme_no_xaxis | Man page Source code |
| theme_no_yaxis | Man page Source code |
| theme_pubr | Man page Source code |
| transferModal | Source code |
| transfer_azimuth | Source code |
| transfer_prev_annot | Man page Source code |
| transfer_symphony | Source code |
| tt_to_es | Source code |
| unmerge_clusters | Source code |
| uploadBulkModal | Source code |
| validate_bulk_labels | Source code |
| validate_bulk_name | Source code |
| validate_bulk_uploads | Source code |
| validate_custom_query | Man page Source code |
| validate_integration | Man page Source code |
| validate_metric | Man page Source code |
| validate_not_path | Source code |
| validate_pdata | Man page Source code |
| validate_preds | Man page Source code |
| validate_scseq_add_sample | Source code |
| validate_scseq_import | Source code |
| validate_subset | Source code |
| validate_up_annot | Man page Source code |
| validate_up_custom | Man page Source code |
| validate_up_meta | Source code |
| volcanoPlotOutput | Source code |
| volcanoPlotUI | Source code |
| write.csv.safe | Source code |
