Man pages for hms-dbmi/drugseqr
Finds CMAP02/L1000 Compounds That Oppose Gene Expression Signatures.

add_adjustedAdd expression data adjusted for pairs/surrogate variables
add_combined_metricsAdd QC metrics to integrated SingleCellExperiment
add_doublet_scoreCalculate doublet score for each cell
add_esAdd metaMA effectsize values to top table.
add_hvgsGet top highly variable genes for subsequent dimensionality...
add_integrated_ambientMark ambient outliers in combined dataset
add_linkoutAdd linkout HTML
add_scseq_clustersCluster SingleCellExperiment
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
add_vsdAdd VST normalized assay data element to expression set
advancedOptionsLogic for advanced options in drugsForm
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 and cell-type...
build_ensdbBuild ensembldb annotation package.
bulkAnalLogic for bulk group analyses for Bulk, Drugs, and Pathways...
bulkAnalInputBulk Differential expression analysis input
bulkAnnotLogic for downloading and uploading bulk annotation
bulkAnnotInputUI for Bulk Data annotation upload/download
bulkCellsPlotlyLogic for Bulk Data cell type deconvolution plotly
bulkDatasetLogic for selected dataset part of bulkFrom
bulkDatasetInputDataset selection input for bulkFormInput
bulkEndTypeLogic for end type selection is bulkFormQuant
bulkExploreTableLogic for differential expression analysis table
bulkFormLogic for Bulk Data form
bulkFormAnalLogic for differential expression analysis part of bulkForm
bulkFormAnalInputDifferential expression analysis inputs for bulkFormInput
bulkFormInputInput form for Bulk Data page
bulkFormQuantLogic for dataset quantification part of bulkForm
bulkFormQuantInputDataset quantification inputs for bulkFormInput
bulkGenePlotlyLogic for Bulk Data gene plotly
bulkMDSLogic for Bulk Data MDS data
bulkMDSplotlyLogic for Bulk Data MDS plotly
bulkPageLogic Bulk Data page
bulkPageUIUI for Bulk Data page
bulkPlotlyUIPlotly MDS output
bulkQuantTableLogic for dataset quantification table
bulkTableTables for datasets page
calcxCalculate x position for correlation plot
check_bulk_changedCheck if newly uploaded pdata is the same as previously...
check_grasCheck Pubchem PUG-View for GRAS notice
check_is_cellrangerDetermine if the selected folder has CellRanger files
clean_yAdjusts expression data for surrogate variables.
clusterComparisonLogic for cluster comparison input
clusterComparisonInputInput form and buttons to select a cluster or contrast and...
collapse_sortedUsed to generate file names for single cell analyses.
CombinePlotsCombine ggplot2-based plots into a single plot
comparisonTypeLogic for comparison type toggle for integrated datasets
comparisonTypeToggleInput form to control/test/all groups for integrated datasets
construct_esetConstruct expression set
construct_path_dfUsed by get_path_df to construct the return result
construct_pbulk_esetsRun pseudo bulk limma fit
construct_pbulk_qcsetsConstruct Pseudobulk QC expression sets
create_scseqLoad kallisto/bustools quantification into a...
customQueryFormLogic for custom query form on Drugs page
customQueryFormInputInput form for custom query on Drugs page
decide_ambientGet ambient genes to exclude
detect_10x_chemistryAuto Detect 10x Chemistry
detect_cellsDetermine non-empty droplets
detect_pairedDetect if experiment is pair-ended.
diff_abundanceRun differential abundance analysis
DimPlotDimensional reduction plot
disableAllDisable multiple ids
distEnhanced Distance Matrix Computation and Visualization
dl_10x_whitelistsDownload 10X whitelists for kallisto bustools correction
dl_pert_pvalsDownload CMAP02/L1000 pert pvals from S3
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)
docsSectionA primary section in the Docs page
docsSideNavNavigation on right side of Docs page
docsSubsectionA subsections of a docsSection
dropdownButtonModified shinyWidgets dropdownButton
dropdownMenuButtonDropdown menu button for dsLabelRowsUI
drugsFormInputInput form for Drugs page
drugsGenesPlotlyLogic query/drug genes plotly
drugsGenesPlotlyOutputUI for query/drug genes plotly
drugsPageLogic for Drugs page
drugsPageUIUI for Drugs page
drugsTableLogic for drug table
drugsTableOutputOutput table for Drugs Page
dtangleFormLogic for deconvolution form
dtangleFormInputInput form for single-cell deconvolution
enableAllEnable multiple ids
evaluate_custom_metricEvaluate custom single-cell metric
exist_clustersTest is there is at lest two clusters
exploreEsetLogic to setup explore_eset for Bulk Data plots
extract_section_infoExtracts info needed to construct docsSideNav
FeaturePlotVisualize 'features' on a dimensional reduction plot
filter_clinicalSubset by clinical phase
filter_genesFilter genes in RNA-seq ExpressionSet
filter_nsigSubset by min signatures
fit_ebayesFit ebayes model
fit_lmRun limma analysis.
fit_lm_scseqFit limma eBayes on single cell RNA-seq dataset
format_dl_annotFormat downloaded annotation
format_query_resFormat perturbation query result like web app.
format_up_annotFormat uploaded annotation
format_up_customFormat uploaded custom query signature
from_crossmetaCovert from crossmeta to drugseqr formats
get_10x_whitepathGet path to 10x whitelist
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_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_ensdb_packageGet ensembldb package name
get_exclude_choicesGet choices for included cluster in integration
get_fastq_id1sGet first sequence identifiers for fastq.gz files
get_founderDetermine the founder of a single-cell dataset
get_gene_choicesAdd cell percents to gene choices for single cell
get_group_levelsGet group levels for bulk data plots
get_gslistGet gslist for pathway analysis
get_gs.namesGet names of gene set
get_integrated_ambientGet genes that are ambient in at least one test and control...
get_kallisto_indexGet path to kallisto index
get_kegg_speciesConvert from species identifier to KEGG species identifier
get_label_plotGet plot to compare original labels for integrated single...
get_label_transfer_choicesGet label transfer choices data.frame
get_mdsGet scalings for MDS plots
get_metric_choicesGet choices data.frame for custom metrics
get_metric_featuresGet features from custom metric
get_modsGet model matrices for surrogate variable analysis
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_outliersFlag outliers
get_paletteGet a pallete for cluster plots
get_path_dfGet data.frame for plotting gene expression values of a...
get_path_directionsGet direction of pathways
get_path_resGet and save pathway results for ebfit object
get_pct_ambientDetermine ambient percent for each gene
get_pkg_versionGet version of salmon/kallisto from system command.
get_pred_annotGet predicted annotation for label transfer
get_query_colsGet query columns
get_sc_dataset_choicesGet data.frame of single-cell dataset choices
get_scseq_markersCombine pairwise wilcox tests between single-cell clusters
get_speciesGet tx2gene for human or mouse depending on intersections
get_topReduce entries in query results
get_top_corsGet top correlated compounds for drug query
get_top_tableGet top table
get_tsne_coordsGet median x-y coordinates for clusters in TSNE plot data
get_tx2geneGet transcript to gene map.
get_wikipediaExtract Wikipedia URL from PUG-View
GetXYAestheticsGet X and Y aesthetics from a plot for a certain geom
heatplotPlot heatmap for genes from goana/kegga analysis
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
import_quantsImport kallisto quants
init_drugseqrInitialize drugseqr folders/files for a new app
integrate_saved_scseqsIntegrate previously saved SingleCellExperiments
integrate_scseqsIntegrate multiple scRNA-seq samples
integrationFormLogic for integration form toggled by showIntegration
integrationFormInputInput form for integrating single cell datasets
interpretCheck safety of evaluating string as R code.
iqr_replicatesRemoves features with replicated annotation.
is_invertibleCheck uploaded bulk pdata to make sure the study design is...
isTruthyAllCheck truthiness of multiple objects
justifiedButtonGroupFull width button group with validation
LabelClustersLabel clusters on a ggplot2-based scatter plot
labelTransferFormLogic for label transfer between datasets
labelTransferFormInputInput form for transfering labels between single cell...
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_scseqLoad SingleCellExperiment
load_scseq_datasetsGenerate data.frame of integrated single cell RNA-Seq...
load_scseq_qcgenesLoad mitochondrial and ribsomal gene names
load_scseq_subsetsLoad subsets of scseqs for integration/subsetting
load_seqLoad bulk RNA-Seq data into an ExpressionSet.
merge_linkoutsMerge columns with image links
navbarUIUI for navbar
NoLegendRemoves the legend
normalize_scseqUtility wrapper to run normalization and log transformation
pairwise_wilcoxRun pairwise wilcox tests between single cell clusters
plot_biogpsPlot BioGPS data for a HGNC symbol
plot_cluster_labelsGenerate plotly for cluster origins of integrated dataset
plot_dprimesGenerate plotly of dprimes values for Drugs tab.
plotlyMDSPlot MDS plotlys
plot_ridgePlot single-cell ridgeline plots
plot_scseq_dprimesPlot dprimes for integrated single-cell dataset with...
plot_tsne_clusterPlot TSNE coloured by cluster
plot_tsne_featurePlot TSNE coloured by gene or QC metric
plot_tsne_feature_sampleFormat gene plots for sample comparison for drugseqr app
process_raw_scseqProcess Count Data for App
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
readRDS.safeRead RDS file safely
remove_bulk_analsRemove analysis info from anals dataframe
remove_dataset_filesDelete stale dataset files after changing sample groups or...
remove_svaRun surrogate variable analysis and factor out surrogate...
rightClickMenuCustom right click menu for selecting correlation point as...
run_custom_queryRun custom query
run_dreamRun dream mixed effect model on RNA-seq ExpressionSet
run_drug_queriesRun drug queries
run_drugseqrRun drugseqr app
run_fastmnnRun fastMNN integration
run_harmonyRun harmony integration
run_kallisto_bulkRuns kallisto quantification for bulk samples.
run_kallisto_scseqRun kallisto/bustools for quantifying 10X scRNA-seq data
run_kallisto_scseq_commandsRuns kallisto scseq commands
run_ligerRun liger integration
run_limmaLinear model fitting of eset with limma.
run_limma_scseqRun limma fit for clusters in single cell RNA-Seq dataset
run_lmfitPerform lmFit analysis from limma.
run_salmon_bulkRuns salmon quantification.
run_scseq_qcRun quality control for single-cell dataset
run_svaRun surrogate variable analysis
run_tsneRun TSNE
run_varPartRun variance partition on RNA-seq ExpressionSet
save_bulk_analsSave new analysis info to anals dataframe
save_lmfitSave lmfit result to disk
save_scleSave SingleCellExperiment as loom file
save_scseq_argsSave arguments for integration/subsetting
save_scseq_dataSave Single Cell RNA-seq data for app
scBioGpsPlotLogic for BioGPS plot
scBioGpsPlotOutputOutput plot of biogps data for a gene
scClusterPlotLogic for cluster plots
scClusterPlotOutputOutput plot of single cell clusters
sc_dl_filenameUtility to generate filename for single cell download csv
scFormLogic for form on Single Cell Exploration page
scFormInputInput form for Single Cell Exploration page
scLabelsComparisonLogic for selecting cluster to plot label origin for...
scLabelsPlotLogic for labels plot for integrated dataset
scLabelsPlotOutputOutput plotly for labels comparison with integrated datasets
scMarkerPlotLogic for marker feature plots
scMarkerPlotOutputOutput plot of single cell markers
scPageLogic for Single Cell Exploration page
scPageUIUI for Single Cell Exploration page
scRidgePlotLogic for Ridge plot for clusters
scRidgePlotOutputOutput Ridgeline plot
scSampleComparisonLogic for single cell cluster analyses for Single Cell,...
scSampleComparisonInputInput for Single Cell analysis
scSampleMarkerPlotLogic for single-cell sample comparison plots
scSampleMarkerPlotOutputOutput plot/plotly for samples comparison with integrated...
scSelectedDatasetLogic for selected dataset part of scForm
scSelectedDatasetInputInput form/associated buttons for selecting single cell...
scseq_part_pathGet path to saved scseq part
select_contrastSelect contrast for an experiment.
selectedAnalLogic for selected dataset/analysis in Drugs tab
selectedAnalInputAnalysis input for Drugs page
selectedAnnotDatasetInputInput for selecting datasets to show original labels for
selectedDrugStudyLogic for selected drug study in drugsForm
selectedDrugStudyInputSelect drugs study (CMAP or L1000) for drugs page
selectedGeneLogic for selected gene to show plots for
selectedGeneInputInput form to select gene for scBioGpsPlotOutput and...
selectedPertSignatureLogic for showing pert selection for gene plot
selectedPertSignatureInputUI for seperate drugsPertInput for CMAP/L1000
select_pairsSelect pairs and replicates for an experiment.
setup_fdataSetup feature annotation data
shorten_cluster_labelsShorted cluster labels when there are lots of clusters
SingleDimPlotPlot a single dimension
sort_query_table_clinfinal sorting/filtering of query table
standardize_cellrangerRename CellRanger files for loading by Read10X
subsetFormLogic for subsetting a datatset
subsetFormInputInput form for subsetting single cell datasets
subset_saved_scseqSubset previously saved SingleCellExperiment
summarise_query_tableSummarise annotated query table
summarize_compoundSummarize query results and annotations by perturbation
supress.genesMove genes to bottom of markers data.frame
svaButtonButton with sliders for adjusting number of surrogate...
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
validate_custom_queryValidate custom query
validate_integrationValidate dataset selection for integration
validate_metricValidate a custom metric
validate_pairsValidate sample pairing for pair-ended RNA seq
validate_pdataValidate pdata before differential expression analysis
validate_predsCheck that label predictions aren't from overwritten datasets
validate_repsValidate sample replicates for RNA seq
validate_up_annotValidate uploaded bulk annotation
validate_up_customValidate uploaded custom query
hms-dbmi/drugseqr documentation built on Aug. 8, 2020, 2:03 a.m.