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

Global functions
AutoPointSize Man page Source code
BlendMap Source code
CheckDots Source code
CombinePlots Man page Source code
DimPlot Man page Source code
ExtractField Source code
FeatureHeatmap Man page
FeaturePlot Man page Source code
GetXYAesthetics Man page Source code
ICAPlot Man page
LabelClusters Man page Source code
Melt Source code
NoLegend Man page Source code
PCAPlot Man page
RandomName Source code
Read10X Man page Source code
Read10X_h5 Man page Source code
SetQuantile Source code
SingleDimPlot Man page Source code
TSNEPlot Man page
`%iff%` Source code
add_adjusted Man page Source code
add_combined_metrics Man page Source code
add_doublet_score Man page Source code
add_es Man page Source code
add_hvgs Man page Source code
add_integrated_ambient Man page Source code
add_linkout Man page
add_qc_genes Source code
add_scseq_clusters Man page 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 Man page Source code
advancedOptions Man page Source code
advancedOptionsInput Man page Source code
annot_query_res Man page Source code
append_annot Man page
boxPlotly Man page Source code
build_ensdb Man page Source code
bulkAnal Man page Source code
bulkAnalInput Man page Source code
bulkAnnot Man page Source code
bulkAnnotInput Man page Source code
bulkCellsPlotly Man page Source code
bulkDataset Man page Source code
bulkDatasetInput Man page Source code
bulkEndType Man page Source code
bulkExploreTable Man page Source code
bulkForm Man page Source code
bulkFormAnal Man page Source code
bulkFormAnalInput Man page Source code
bulkFormInput Man page Source code
bulkFormQuant Man page Source code
bulkFormQuantInput Man page Source code
bulkGenePlotly Man page Source code
bulkMDS Man page Source code
bulkMDSplotly Man page Source code
bulkPage Man page Source code
bulkPageUI Man page Source code
bulkPlotlyUI Man page Source code
bulkQuantTable Man page Source code
bulkTable Man page Source code
calcx Man page
check_bulk_changed Man page Source code
check_gras Man page Source code
check_is_cellranger Man page Source code
clean_y Man page Source code
clusterComparison Man page Source code
clusterComparisonInput Man page Source code
collapse_sorted Man page Source code
comparisonType Man page Source code
comparisonTypeToggle Man page Source code
construct_eset Man page Source code
construct_path_df Man page Source code
construct_pbulk_esets Man page Source code
construct_pbulk_qcsets Man page Source code
create_scseq Man page Source code
customQueryForm Man page Source code
customQueryFormInput Man page Source code
decide_ambient Man page Source code
detect_10x_chemistry Man page Source code
detect_cells Man page Source code
detect_paired Man page Source code
diff_abundance Man page Source code
disableAll Man page Source code
dist Man page
dl_10x_whitelists Man page Source code
dl_pert_pvals Man page Source code
dl_pert_result Man page Source code
dl_pert_signature Man page Source code
docsPageUI Man page Source code
docsSection Man page Source code
docsSideNav Man page Source code
docsSubsection Man page Source code
dropdownButton Man page Source code
dropdownMenuButton Man page Source code
drugsForm Source code
drugsFormInput Man page Source code
drugsGenesPlotly Man page Source code
drugsGenesPlotlyOutput Man page Source code
drugsPage Man page Source code
drugsPageUI Man page Source code
drugsTable Man page Source code
drugsTableOutput Man page Source code
dsLabelRowsUI Source code
dtangleForm Man page Source code
dtangleFormInput Man page Source code
enableAll Man page Source code
evaluate_custom_metric Man page Source code
exist_clusters Man page Source code
exploreEset Man page Source code
extract_geneSets Source code
extract_section_info Man page Source code
filter_clinical Man page Source code
filter_genes Man page Source code
filter_nsig Man page Source code
fit_ebayes Man page Source code
fit_lm Man page Source code
fit_lm_scseq Man page Source code
format_dl_annot Man page 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
get_10x_whitepath 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_cluster_choices Man page Source code
get_cluster_markers Man page Source code
get_cluster_stats Man page 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_ensdb_package Man page Source code
get_exclude_choices Man page Source code
get_fastq_id1s Man page Source code
get_founder Man page Source code
get_gene_choices Man page Source code
get_group_levels Man page Source code
get_gs.names Man page Source code
get_gslist Man page Source code
get_integrated_ambient Man page Source code
get_kallisto_index Man page Source code
get_kegg_species Man page Source code
get_label_plot Man page Source code
get_label_transfer_choices Man page Source code
get_mds Man page Source code
get_metric_choices Man page Source code
get_metric_features Man page Source code
get_mods Man page Source code
get_nearest_row Man page Source code
get_npc_choices Man page Source code
get_open_a Man page
get_outliers Man page Source code
get_palette Man page Source code
get_path_df Man page Source code
get_path_directions Man page Source code
get_path_res Man page Source code
get_pathway_names Source code
get_pct_ambient Man page Source code
get_pkg_version Man page Source code
get_pred_annot Man page Source code
get_query_cols Man page Source code
get_sc_dataset_choices Man page Source code
get_scseq_markers Man page Source code
get_species Man page Source code
get_top Man page Source code
get_top_cors Man page
get_top_table Man page Source code
get_tsne_coords Man page Source code
get_tx2gene Man page Source code
get_wikipedia Man page Source code
heatplot Man page Source code
html_space Man page Source code
id_from_tab Man page Source code
identify_sc_files Man page Source code
import_quants Man page Source code
init_drugseqr Man page Source code
integrate_saved_scseqs Man page Source code
integrate_scseqs Man page Source code
integrationForm Man page Source code
integrationFormInput Man page Source code
interpret Man page Source code
iqr_replicates Man page Source code
is.installed Source code
isTruthyAll Man page Source code
is_invertible Man page Source code
justifiedButtonGroup Man page Source code
labelTransferForm Man page Source code
labelTransferFormInput Man page Source code
limit_cells Man page Source code
load_bulk_anals Man page Source code
load_bulk_datasets Man page Source code
load_cellranger_counts Man page 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_raw_scseq Man page Source code
load_scseq Man page Source code
load_scseq_datasets Man page Source code
load_scseq_qcgenes Man page Source code
load_scseq_subsets Man page Source code
load_seq Man page Source code
merge_linkouts Man page
navbarUI Man page Source code
normalize_scseq Man page Source code
pairwise_wilcox Man page Source code
plot_biogps Man page Source code
plot_cluster_labels Man page Source code
plot_dprimes Man page Source code
plot_ridge Man page Source code
plot_scseq_dprimes Man page Source code
plot_tsne_cluster Man page Source code
plot_tsne_feature Man page Source code
plot_tsne_feature_sample Man page Source code
plotlyMDS Man page Source code
process_cellranger_counts Source code
process_raw_scseq Man page Source code
query_budger Man page Source code
query_drugs Man page Source code
readRDS.safe Man page Source code
remove_bulk_anals Man page Source code
remove_dataset_files Man page Source code
remove_sva Man page Source code
rightClickMenu Man page Source code
run_custom_query Man page Source code
run_dream Man page Source code
run_drug_queries Man page Source code
run_drugseqr Man page Source code
run_fastmnn Man page Source code
run_harmony Man page Source code
run_kallisto_bulk Man page Source code
run_kallisto_scseq Man page Source code
run_kallisto_scseq_commands Man page Source code
run_liger Man page Source code
run_limma Man page
run_limma_scseq Man page Source code
run_lmfit Man page Source code
run_salmon_bulk Man page Source code
run_scseq_qc Man page Source code
run_sva Man page Source code
run_tsne Man page Source code
run_varPart Man page Source code
sammon Source code
save_bulk_anals Man page Source code
save_lmfit Man page Source code
save_scle Man page Source code
save_scseq_args Man page Source code
save_scseq_data Man page Source code
scBioGpsPlot Man page Source code
scBioGpsPlotOutput Man page Source code
scClusterPlot Man page Source code
scClusterPlotOutput Man page Source code
scForm Man page Source code
scFormInput Man page Source code
scLabelsComparison Man page Source code
scLabelsPlot Man page Source code
scLabelsPlotOutput Man page Source code
scMarkerPlot Man page Source code
scMarkerPlotOutput Man page Source code
scPage Man page Source code
scPageUI Man page Source code
scRidgePlot Man page Source code
scRidgePlotOutput Man page Source code
scSampleComparison Man page Source code
scSampleComparisonInput Man page Source code
scSampleMarkerPlot Man page Source code
scSampleMarkerPlotOutput Man page Source code
scSelectedDataset Man page Source code
scSelectedDatasetInput Man page Source code
sc_dl_filename Man page Source code
scseq_part_path Man page Source code
select_contrast Man page Source code
select_pairs Man page Source code
selectedAnal Man page Source code
selectedAnalInput Man page Source code
selectedAnnotDatasetInput Man page Source code
selectedDrugStudy Man page Source code
selectedDrugStudyInput Man page Source code
selectedGene Man page Source code
selectedGeneInput Man page Source code
selectedPertSignature Man page Source code
selectedPertSignatureInput Man page Source code
setup_fdata Man page Source code
shorten_cluster_labels Man page Source code
sort_query_table_clin Man page
standardize_cellranger Man page Source code
subsetForm Man page Source code
subsetFormInput Man page Source code
subset_saved_scseq Man page Source code
summarise_query_table Man page Source code
summarize_compound Man page Source code
supress.genes Man page Source code
svaButton Man page 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
validate_custom_query Man page Source code
validate_integration Man page Source code
validate_metric Man page Source code
validate_pairs Man page Source code
validate_pdata Man page Source code
validate_preds Man page Source code
validate_reps Man page Source code
validate_up_annot Man page Source code
validate_up_custom Man page Source code
hms-dbmi/drugseqr documentation built on Aug. 8, 2020, 2:03 a.m.