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

Global functions
AutoPointSize Man page Source code
BlendMap Source code
CheckDots Man page 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
NNTransform 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
SingleExIPlot Man page Source code
TSNEPlot Man page
VlnPlot Source code
`%iff%` Source code
add_adjusted Source code
add_combined_ambience Source code
add_combined_metrics Man page Source code
add_doublet_score Man page Source code
add_hvgs Man page Source code
add_integrated_ambient Man page Source code
add_linkout Man page
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_across_cells Source code
annot_query_res Man page Source code
append_annot Man page
attach_clusters Source code
attach_meta 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
bulkEndType Source code
bulkExploreTable Source code
bulkForm Source code
bulkFormAnal Source code
bulkFormAnalInput Source code
bulkFormInput Source code
bulkFormQuant Source code
bulkFormQuantInput Source code
bulkGenePlotly Source code
bulkMDS Source code
bulkMDSplotly Source code
bulkPage Man page Source code
bulkPageUI Man page Source code
bulkPlotlyUI Source code
bulkQuantTable Source code
bulkTable Source code
calc_cluster_ambience Source code
calcx Man page
check_bulk_changed Man page Source code
check_gras Man page Source code
check_has_scseq Source code
check_is_cellranger Man page Source code
clusterComparison Source code
clusterComparisonInput Source code
clusterPlots Source code
col2hex Source code
collapse_sorted Man page Source code
comparisonType Source code
comparisonTypeToggle Source code
confirmModal Source code
construct_path_df Man page Source code
construct_pbulk_qcsets Man page Source code
construct_pbulk_subsets Man page Source code
construct_top_markers Source code
create_scseq Man page Source code
customQueryForm Source code
customQueryFormInput Man page Source code
datasets_to_list Man page Source code
deleteModal Source code
detect_10x_chemistry Man page Source code
detect_cells Man page Source code
dgc_to_dgr Source code
diff_abundance Man page Source code
disableAll Man page Source code
dl_10x_whitelists Man page Source code
dl_pert_result Man page Source code
dl_pert_signature Man page Source code
docsPageUI Man page Source code
docsSection Source code
docsSideNav Source code
docsSubsection Source code
downsample_clusters Man page Source code
downsample_group 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
dtangleForm Source code
dtangleFormInput Source code
enableAll Man page Source code
es_to_tt Source code
evaluate_custom_metric Man page Source code
exist_clusters Man page Source code
exploreEset Source code
extract_enids Source code
extract_section_info Source code
fast_dgr_row Source code
file.move Source code
filter_clinical Man page Source code
filter_nsig Man page Source code
fit_lm Source code
format_dl_annot Man page Source code
format_query_res Man page Source code
format_ridge_annot 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
frows Source code
get_10x_whitepath Man page Source code
get_abundance_diff Source code
get_ambience Man page Source code
get_azimuth_cols Source code
get_azimuth_resoln 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_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_exclude_cells Source code
get_exclude_dirs Man page Source code
get_founder Man page Source code
get_gene_diff Source code
get_gene_table Source code
get_genego Man page Source code
get_gonames Man page Source code
get_grid Source code
get_group_levels Man page 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_npc_choices Man page Source code
get_open_a Man page
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_ptsize Source code
get_qc_table Source code
get_query_cols Man page Source code
get_resoln_dir Source code
get_resoln_name Man page Source code
get_ridge_data Man page Source code
get_sc_dataset_choices Man page Source code
get_scdata_type Source code
get_snn_graph Source code
get_species Man page Source code
get_top Man page Source code
get_top_cors Man page
get_tsne_coords 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
html_space Man page Source code
id_from_tab Man page Source code
identify_sc_files Man page Source code
init_dseqr Man page Source code
integrate_saved_scseqs Man page Source code
integrate_scseqs Man page Source code
integrationForm Source code
integrationFormInput Source code
interpret Man page Source code
iqr_replicates Source code
is.numstring 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
labelTransferForm Source code
labelTransferFormInput Source code
limit_cells Man page Source code
load_args 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_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
merge_linkouts Man page
name_list Source code
navbar2UI Man page Source code
navbarUI Man page Source code
normalize_scseq Man page Source code
plot_biogps Man page Source code
plot_cluster Man page Source code
plot_dprimes Man page
plot_feature Man page Source code
plot_feature_sample Man page Source code
plot_scseq_diff Source code
plot_scseq_dprimes Man page Source code
plotlyMDS Man page Source code
process_cellranger_counts Source code
process_raw_scseq Man page Source code
qread.safe Man page Source code
query_budger Man page Source code
query_drugs Man page Source code
range02 Source code
remove_bulk_anals Man page Source code
remove_dataset_files Man page Source code
resize_points Source code
resolutionForm Source code
resolutionFormInput Source code
rightClickMenu Man page Source code
run_azimuth Source code
run_custom_query Man page Source code
run_drug_queries Man page Source code
run_dseqr Man page 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_integrate_saved_scseqs Man page Source code
run_kallisto_bulk_bg Source code
run_kallisto_scseq Man page Source code
run_kallisto_scseq_commands Man page Source code
run_limma_scseq Man page Source code
run_load_raw_scseq 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
safe.fun Source code
sammon Source code
save_azimuth_clusters Source code
save_bulk_anals Man page Source code
save_lmfit Man page Source code
save_scseq_args Man page Source code
save_scseq_data Man page Source code
scAbundancePlot Source code
scAbundancePlotOutput Source code
scBioGpsPlot Source code
scBioGpsPlotOutput Source code
scClusterPlot Source code
scClusterPlotOutput Source code
scForm Source code
scFormInput Source code
scLabelsComparison Source code
scMarkerPlot Source code
scMarkerPlotOutput Source code
scPage Man page Source code
scPageUI Man page Source code
scRidgePlot Source code
scRidgePlotOutput 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
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
shorten_cluster_labels Man page Source code
shorten_y Source code
simplify Source code
sort_query_table_clin Man page
split_save_scseq Source code
split_scseq Source code
standardize_cellranger Man page Source code
subsetForm Source code
subsetFormInput 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
transfer_azimuth Source code
transfer_prev_annot Man page Source code
transition_efs Man page Source code
tt_to_es Source code
update_cluster_plot Source code
update_feature_plot Man page Source code
uploadModal Source code
validate_custom_query Man page Source code
validate_integration Man page Source code
validate_metric Man page Source code
validate_pdata Man page Source code
validate_preds Man page 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
warnApplyModal Source code
write.csv.safe Source code
zoom_plot Source code
hms-dbmi/drugseqr documentation built on July 19, 2021, 1:10 p.m.