Man pages for hms-dbmi/drugseqr
GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

add_combined_metricsAdd QC metrics to integrated SingleCellExperiment
add_doublet_scoreCalculate doublet score for each cell
add_hvgsGet top highly variable genes for subsequent dimensionality...
add_integrated_ambientMark ambient outliers in combined dataset
add_linkoutAdd linkout HTML
add_scseq_qc_metricsCalculate QC metrics for SingleCellExperiment
add_scseq_qcplot_metricsAdd QC metrics to SingleCellExperiment for plotting
add_table_htmlAdd HTML to query results table
advancedOptionsInputadvanced options input for drugs page
annot_query_resAnnotate query result
append_annotBind annotation data to pdata
AutoPointSizeAutomagically calculate a point size for ggplot2-based...
boxPlotlyGenerate boxplotly for vsd normalized gene plots.
boxPlotlyCellsGenerate boxplotly for cell type deconvolution plots.
bulkPageLogic for Bulk Data Tab
bulkPageUIUI for Bulk Data page
calcxCalculate x position for correlation plot
check_bulk_changedCheck if newly uploaded pdata is the same as previously...
CheckDotsCheck the use of ...
check_grasCheck Pubchem PUG-View for GRAS notice
check_is_cellrangerDetermine if the selected folder has CellRanger files
collapse_sortedUsed to generate file names for single cell analyses.
CombinePlotsCombine ggplot2-based plots into a single plot
construct_path_dfUsed by get_path_df to construct the return result
construct_pbulk_qcsetsConstruct Pseudobulk QC expression sets
construct_pbulk_subsetsRun pseudo bulk limma fit
create_scseqLoad kallisto/bustools quantification into a...
customQueryFormInputInput form for custom query on Drugs page
datasets_to_listConvert single-cell datasets data.frame to list
detect_10x_chemistryAuto Detect 10x Chemistry
detect_cellsDetermine non-empty droplets
diff_abundanceRun differential abundance analysis
DimPlotDimensional reduction plot
disableAllDisable multiple ids
dl_10x_whitelistsDownload 10X whitelists for kallisto bustools correction
dl_pert_resultDownload CMAP02/L1000 pert query result from S3
dl_pert_signatureDownload CMAP02/L1000 pert signature from S3
docsPageUIUI for docs page (add new sections here)
downsample_clustersDownsample SingleCellExperiment clusters
downsample_groupDownsample cells within each cluster across a group
dropdownButtonModModified shinyWidgets dropdownButton
dropdownMenuButtonDropdown menu button for dsLabelRowsUI
drugsFormInputInput form for Drugs page
drugsGenesPlotlyOutputUI for query/drug genes plotly
drugsPageLogic for Drugs Tab
drugsPageUIUI for Drugs page
drugsTableOutputOutput table for Drugs Page
enableAllEnable multiple ids
evaluate_custom_metricEvaluate custom single-cell metric
exist_clustersTest is there is at lest two clusters
FeaturePlotVisualize 'features' on a dimensional reduction plot
filter_clinicalSubset by clinical phase
filter_nsigSubset by min signatures
format_dl_annotFormat downloaded annotation
format_query_resFormat perturbation query result like web app.
format_ridge_annotAdd cluster numbers to annotation
format_up_annotFormat uploaded annotation
format_up_customFormat uploaded custom query signature
from_crossmetaCovert from crossmeta to dseqr formats
get_10x_whitepathGet path to 10x whitelist
get_ambienceGet genes that are ambient in at least one test and control...
get_boxplotly_cell_argsGet arguments for cells boxplotly
get_boxplotly_gene_argsGet arguments for gene boxplotly
get_cell_choicesGet cell choices data.frame for CMAP02 or L1000
get_cluster_choicesGet cluster choices data.frame for selectize dropdown
get_cluster_markersLoads markers for single cell cluster
get_cluster_statsGet/Save cluster stats for single-cell related...
get_contrast_choicesGet contrast choices data.frame for selectize dropdown
get_contrast_markersGet markers for one cluster against one other cluster
get_cors_htmlGet HTML for correlation values.
get_distEnhanced Distance Matrix Computation and Visualization
get_dprimesGet dprime effect size values.
get_drugbankExtract DrugBank URL from PUG-View
get_drug_pathsGet file paths to drug query results
get_drugs_tableGet Drugs metadata table for CMAP02 or L1000
get_exclude_dirsGet single-cell directories without fastq or cellranger files
get_founderDetermine the founder of a single-cell dataset
get_genegoGet gene to GO map for pathway analysis
get_gonamesGet names of gene set
get_group_levelsGet group levels for bulk data plots
get_label_transfer_choicesGet label transfer choices data.frame
get_mdsGet scalings for MDS plots
get_metric_choicesGet choices data.frame for custom metrics (for subsetting)
get_metric_featuresGet features from custom metric
get_nearest_rowSearch for closest row in a truth matrix for each row in a...
get_npc_choicesGet number of clusters different number of PCs
get_open_aGet Opening HTML a Tag
get_paletteGet a pallete for cluster plots
get_path_dfGet data.frame for plotting gene expression values of a...
get_path_resGet and save pathway results for ebfit object
get_pred_annotGet predicted annotation for label transfer
get_presto_markersGet cluster markers using presto
get_query_colsGet query columns
get_resoln_nameGet the applied resolution dataset name
get_ridge_dataGet data for single-cell ridgeline plots
get_sc_dataset_choicesGet data.frame of single-cell dataset choices
get_speciesGet species for human or mouse depending on gene ids
get_topReduce entries in query results
get_top_corsGet top correlated compounds for drug query
get_tsne_coordsGet median x-y coordinates for clusters in TSNE plot data
get_wikipediaExtract Wikipedia URL from PUG-View
GetXYAestheticsGet X and Y aesthetics from a plot for a certain geom
handle_sc_progressUpdate Progress from Background Processes
html_spaceFormat character vectors that will be recognized by HTML
identify_sc_filesGet 10X FastQ paths for a read type and sort by increasing...
id_from_tabConvert tab name to formated id
init_dseqrInitialize dseqr folders/files for a new app
integrate_saved_scseqsIntegrate previously saved SingleCellExperiments
integrate_scseqsIntegrate multiple scRNA-seq samples
interpretCheck safety of evaluating string as R code.
is_invertibleCheck uploaded bulk pdata to make sure the study design is...
isTruthyAllCheck truthiness of multiple objects
justifiedButtonGroupFull width button group with validation
keep_curr_selectedTake currently selected row and keep it in the same position
LabelClustersLabel clusters on a ggplot2-based scatter plot
limit_cellsLimit Query Results to Specific Cell Lines
load_bulk_analsLoad previous bulk anals dataframe
load_bulk_datasetsLoad previous bulk datasets dataframe
load_cellranger_countsLoad cell ranger counts
load_custom_analsLoad data.frame of custom anals for selectizeInput
load_custom_resultsLoad results of previous custom query
load_drug_esLoad drug effect size matrices for drug queries
load_kallisto_countsRead kallisto/bustools market matrix and annotations
load_pert_analsLoad data.frame of CMAP02/L1000 perturbations for right click...
load_pert_signatureGet perturbation signature
load_raw_scseqProcess raw single cell fastq or cellranger files for app
load_resolnLoad the applied resolution name
load_scseq_datasetsGenerate data.frame of integrated single cell RNA-Seq...
load_scseq_qcgenesLoad mitochondrial and ribsomal gene names
load_scseq_qsLoad SingleCellExperiment from qs file
load_scseq_subsetsLoad subsets of scseqs for integration/subsetting
merge_linkoutsMerge columns with image links
navbar2UIUI for secondary navbar
navbarUIUI for navbar
NoLegendRemoves the legend
normalize_scseqUtility wrapper to run normalization and log transformation
plot_biogpsPlot BioGPS data for a HGNC symbol
plot_clusterPlot TSNE coloured by cluster
plot_dprimesGenerate plotly of dprimes values for Drugs tab.
plot_featurePlot TSNE coloured by gene or QC metric
plot_feature_sampleFormat gene plots for sample comparison for dseqr app
plotlyMDSPlot MDS plotlys
plot_scseq_dprimesPlot dprimes for integrated single-cell dataset with...
process_raw_scseqProcess Count Data for App
qread.safeRead qs file safely
query_budgerFind drugs that maximally affect a selection of genes
query_drugsGet correlation between query and drug signatures.
Read10XLoad in data from 10X
Read10X_h5Read 10X hdf5 file
remove_bulk_analsRemove analysis info from anals dataframe
remove_dataset_filesDelete stale dataset files after changing sample groups or...
rightClickMenuCustom right click menu for selecting correlation point as...
run_custom_queryRun custom query
run_drug_queriesRun drug queries
run_dseqrRun dseqr app
run_fastmnnRun fastMNN integration
run_harmonyRun harmony integration
run_integrate_saved_scseqsIntegration Utility Function for Background Process
run_kallisto_scseqRun kallisto/bustools for quantifying 10X scRNA-seq data
run_kallisto_scseq_commandsRuns kallisto scseq commands
run_limma_scseqRun limma on pseudobulk experiment
run_pcaCluster SingleCellExperiment
run_post_clusterPost-Cluster Processing of SingleCellExperiment
run_reductionRun TSNE or UMAP
run_scseq_qcRun quality control for single-cell dataset
save_bulk_analsSave new analysis info to anals dataframe
save_lmfitSave lmfit result to disk
save_scseq_argsSave arguments for integration/subsetting
save_scseq_dataSave Single Cell RNA-seq data for app
sc_dl_filenameUtility to generate filename for single cell download csv
scPageLogic for Single Cell Tab
scPageUIUI for Single Cell Exploration page
scseq_part_pathGet path to saved scseq part
selectedAnalInputAnalysis input for Drugs page
selectedDrugStudyInputSelect drugs study (CMAP or L1000) for drugs page
selectedPertSignatureInputUI for seperate drugsPertInput for CMAP/L1000
shorten_cluster_labelsShorted cluster labels when there are lots of clusters
SingleDimPlotPlot a single dimension
SingleExIPlotPlot a single expression by identity on a plot
sort_query_table_clinfinal sorting/filtering of query table
standardize_cellrangerRename CellRanger files for loading by Read10X
subset_saved_scseqSubset SingleCellExperiment
summarise_query_tableSummarise annotated query table
summarize_compoundSummarize query results and annotations by perturbation
tabPaneUI for a tab pane
theme_dimgrayMake ggplot axes and text dimgray
theme_no_xaxisRemove ggplot xaxis title, text, and ticks
theme_no_yaxisRemove ggplot yaxis title, text, and ticks
theme_pubrPublication ready theme
transfer_prev_annotTransfer annotation when change resolution
transition_efsUtility to move files on EFS from IA to SA
update_feature_plotUpdate Feature Plot
validate_custom_queryValidate custom query
validate_integrationValidate dataset selection for integration
validate_metricValidate a custom metric
validate_pdataValidate pdata before differential expression analysis
validate_predsCheck that label predictions aren't from overwritten datasets
validate_up_annotValidate uploaded bulk annotation
validate_up_customValidate uploaded custom query
hms-dbmi/drugseqr documentation built on July 19, 2021, 1:10 p.m.