Man pages for hms-dbmi/drugseqr
GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations
| add_cluster_numbers | Add cluster numbers to annotation |
| add_combined_metrics | Add QC metrics to integrated SingleCellExperiment |
| add_doublet_score | Calculate doublet score for each cell |
| add_hvgs | Add top highly variable genes for subsequent dimensionality... |
| add_linkout | Add linkout HTML |
| add_scseq_qc_metrics | Calculate QC metrics for SingleCellExperiment |
| add_scseq_qcplot_metrics | Add QC metrics to SingleCellExperiment for plotting |
| add_table_html | Add HTML to query results table |
| advancedOptionsInput | advanced options input for drugs page |
| aggregate.Matrix | Compute summary statistics of a Matrix |
| annot_query_res | Annotate query result |
| append_annot | Bind annotation data to pdata |
| boxPlotly | Generate boxplotly for vsd normalized gene plots. |
| boxPlotlyCells | Generate boxplotly for cell type deconvolution plots. |
| bulkPage | Logic for Bulk Data Tab |
| bulkPageUI | UI for Bulk Data page |
| calcx | Calculate x position for correlation plot |
| check_bulk_changed | Check if newly uploaded pdata is the same as previously... |
| check_gras | Check Pubchem PUG-View for GRAS notice |
| check_has_scseq | Check if folder has single-cell files |
| check_is_market_matrix | Determine if the selected folder has cellranger market matrix... |
| clean_kb_scseq | Clean up kb output directory |
| collapse_sorted | Used to generate file names for single cell analyses. |
| construct_path_df | Used by get_path_df to construct the return result |
| construct_pbulk_subsets | Run pseudo bulk limma fit |
| create_scseq | Load kallisto/bustools quantification into a... |
| customQueryFormInput | Input form for custom query on Drugs page |
| datasets_to_list | Convert single-cell datasets data.frame to list |
| detect_10x_chemistry | Auto Detect 10x Chemistry |
| detect_cells | Determine non-empty droplets |
| diff_abundance | Run differential abundance analysis |
| dir_exists | Safe dir.exists |
| disableAll | Disable multiple ids |
| dl_pert_result | Download CMAP02/L1000 pert query result from S3 |
| dl_pert_signature | Download CMAP02/L1000 pert signature from S3 |
| download_kb_index | Download pre-built index using kb-python |
| downsample_clusters | Downsample SingleCellExperiment clusters |
| dropdownButtonMod | Modified shinyWidgets dropdownButton |
| dropdownMenuButton | Dropdown menu button for dsLabelRowsUI |
| drugsFormInput | Input form for Drugs page |
| drugsGenesPlotlyOutput | UI for query/drug genes plotly |
| drugsPage | Logic for Drugs Tab |
| drugsPageUI | UI for Drugs page |
| drugsTableOutput | Output table for Drugs Page |
| enableAll | Enable multiple ids |
| evaluate_custom_metric | Evaluate custom single-cell metric |
| file_exists | Safe file.exists |
| filter_clinical | Subset by clinical phase |
| filter_nsig | Subset by min signatures |
| format_dl_annot | Format downloaded annotation |
| format_query_res | Format perturbation query result like web app. |
| format_up_annot | Format uploaded annotation |
| format_up_custom | Format uploaded custom query signature |
| from_crossmeta | Covert from crossmeta to dseqr formats |
| get_ambience | Get sample ambience profiles |
| get_boxplotly_cell_args | Get arguments for cells boxplotly |
| get_boxplotly_gene_args | Get arguments for gene boxplotly |
| get_cell_choices | Get cell choices data.frame for CMAP02 or L1000 |
| get_cluster_choices | Get cluster choices data.frame for selectize dropdown |
| get_cluster_markers | Loads markers for single cell cluster |
| get_cluster_stats | Get and save cluster stats for single-cell related... |
| get_contrast_choices | Get contrast choices data.frame for selectize dropdown |
| get_contrast_markers | Get markers for one cluster against one other cluster |
| get_cors_html | Get HTML for correlation values. |
| getDeleteRowButtons | Get HTML to make delete buttons in datatable rows |
| get_dist | Enhanced Distance Matrix Computation and Visualization |
| get_dprimes | Get dprime effect size values. |
| get_drugbank | Extract DrugBank URL from PUG-View |
| get_drug_paths | Get file paths to drug query results |
| get_drugs_table | Get Drugs metadata table for CMAP02 or L1000 |
| get_expression_colors | Get expression colors for scatterplot |
| get_founder | Determine the founder of a single-cell dataset |
| get_genego | Get gene to GO map for pathway analysis |
| get_gonames | Get names of gene set |
| get_group_levels | Get group levels for bulk data plots |
| get_label_transfer_choices | Get label transfer choices data.frame |
| get_mds | Get scalings for MDS plots |
| get_metric_choices | Get choices data.frame for custom metrics (for subsetting) |
| get_metric_features | Get features from custom metric |
| get_nearest_row | Search for closest row in a truth matrix for each row in a... |
| get_npc_choices | Get number of clusters different number of PCs |
| get_open_a | Get Opening HTML a Tag |
| get_palette | Get a pallete for cluster plots |
| get_path_df | Get data.frame for plotting gene expression values of a... |
| get_path_res | Get and save pathway results for ebfit object |
| get_pred_annot | Get predicted annotation for label transfer |
| get_presto_markers | Get cluster markers using presto |
| get_query_cols | Get query columns |
| get_resoln_name | Get the applied resolution dataset name |
| get_sc_dataset_choices | Get data.frame of single-cell dataset choices |
| get_species | Get species for human or mouse depending on gene ids |
| get_top | Reduce entries in query results |
| get_top_cors | Get top correlated compounds for drug query |
| get_tsne_coords | Get median x-y coordinates for clusters in TSNE plot data |
| get_violin_data | Get data for single-cell violin plots |
| get_wikipedia | Extract Wikipedia URL from PUG-View |
| handle_sc_progress | Update Progress from Background Processes |
| html_space | Format character vectors that will be recognized by HTML |
| identify_sc_files | Get 10X FastQ paths for a read type and sort by increasing... |
| id_from_tab | Convert tab name to formated id |
| import_scseq | Import raw single cell fastq or cellranger files for app |
| init_dseqr | Initialize dseqr folders/files for a new app |
| integrate_saved_scseqs | Integrate previously saved SingleCellExperiments |
| integrate_scseqs | Integrate multiple scRNA-seq samples |
| interpret | Check safety of evaluating string as R code. |
| is_invertible | Check uploaded bulk pdata to make sure the study design is... |
| isTruthy | Truthy and falsy values |
| isTruthyAll | Check truthiness of multiple objects |
| justifiedButtonGroup | Full width button group with validation |
| keep_curr_selected | Take currently selected row and keep it in the same position |
| limit_cells | Limit Query Results to Specific Cell Lines |
| load_bulk_datasets | Load previous bulk datasets dataframe |
| load_cellranger_counts | Load cell ranger counts |
| load_custom_anals | Load data.frame of custom anals for selectizeInput |
| load_custom_results | Load results of previous custom query |
| load_drug_es | Load drug effect size matrices for drug queries |
| load_kallisto_counts | Read kallisto/bustools market matrix and annotations |
| load_pert_anals | Load data.frame of CMAP02/L1000 perturbations for right click... |
| load_pert_signature | Get perturbation signature |
| load_resoln | Load the applied resolution name |
| load_scseq_datasets | Generate data.frame of integrated single cell RNA-Seq... |
| load_scseq_qcgenes | Load mitochondrial and ribsomal gene names |
| load_scseq_qs | Load SingleCellExperiment from qs file |
| load_scseq_subsets | Load subsets of scseqs for integration/subsetting |
| make_unique | Make Character Strings Unique |
| merge_linkouts | Merge columns with image links |
| merge_samples | Merge samples that are from the sample subject |
| navbar2UI | UI for secondary navbar |
| navbarUI | UI for navbar |
| normalize_scseq | Utility wrapper to run normalization and log transformation |
| plot_biogps | Plot BioGPS data for a HGNC symbol |
| plot_dprimes | Generate plotly of dprimes values for Drugs tab. |
| plotlyMDS | Plot MDS plotlys |
| plot_violin | Violin Plot |
| process_raw_scseq | Process Count Data for App |
| qread.safe | Read qs file safely |
| query_budger | Find drugs that maximally affect a selection of genes |
| query_drugs | Get correlation between query and drug signatures. |
| remove_dataset_files | Delete stale dataset files after changing sample groups or... |
| req | Check for required values |
| rightClickMenu | Custom right click menu for selecting correlation point as... |
| run_custom_query | Run custom query |
| run_drug_queries | Run drug queries |
| run_dseqr | Run dseqr app |
| run_fastmnn | Run fastMNN integration |
| run_harmony | Run harmony integration |
| run_integrate_saved_scseqs | Integration Utility Function for Background Process |
| run_kb_scseq | Run kallisto/bustools for quantifying 10X scRNA-seq data |
| run_limma_scseq | Run limma on pseudobulk experiment |
| run_pca | Run PCA on SingleCellExperiment |
| run_post_cluster | Post-Cluster Processing of SingleCellExperiment |
| run_reduction | Run TSNE or UMAP |
| run_scseq_qc | Run quality control for single-cell dataset |
| save_lmfit | Save lmfit result to disk |
| save_scseq_args | Save arguments for integration/subsetting |
| save_scseq_data | Save Single Cell RNA-seq data for app |
| sc_dl_filename | Utility to generate filename for single cell download csv |
| scPage | Logic for Single Cell Tab |
| scPageUI | UI for Single Cell Exploration page |
| scseq_part_path | Get path to saved scseq part |
| selectedAnalInput | Analysis input for Drugs page |
| selectedDrugStudyInput | Select drugs study (CMAP or L1000) for drugs page |
| selectedPertSignatureInput | UI for seperate drugsPertInput for CMAP/L1000 |
| send_slack_error | Send shiny errors to slack |
| SingleViolinIPlot | Violin plot by identity |
| sort_clusters | shortest distance between cluster centroids |
| sort_query_table_clin | final sorting/filtering of query table |
| standardize_cellranger | Rename CellRanger files for loading by Read10X |
| subset_saved_scseq | Subset SingleCellExperiment |
| summarise_query_table | Summarise annotated query table |
| summarize_compound | Summarize query results and annotations by perturbation |
| tabPane | UI for a tab pane |
| theme_dimgray | Make ggplot axes and text dimgray |
| theme_no_xaxis | Remove ggplot xaxis title, text, and ticks |
| theme_no_yaxis | Remove ggplot yaxis title, text, and ticks |
| theme_pubr | Publication ready theme |
| transfer_prev_annot | Transfer annotation when change resolution |
| validate_custom_query | Validate custom query |
| validate_integration | Validate dataset selection for integration |
| validate_metric | Validate a custom metric |
| validate_pdata | Validate pdata before differential expression analysis |
| validate_preds | Check that label predictions aren't from overwritten datasets |
| validate_up_annot | Validate uploaded bulk annotation |
| validate_up_custom | Validate uploaded custom query |
