Man pages for Wang-Cankun/rDeepMAPS
IRIS3-api

active_label	Return active cell idents labels
adt_qc_list	Get QC metrics list for single scRNA-seq dataset
AssociatedDimReducs	Get dimensional reduction information associated with an...
atac_qc_list	Get QC metrics list for single scATAC-seq dataset
BinMean	Calculate mean values of a matrix by bins
calc_deg	Run Seurat clustering
calc_dr	Run DR
calc_enrichr_table	Run Enrichr
calc_gsea_table	Run GSEA enrichment
calc_regulon_gsea_table	Run GSEA enrichment
calc_regulon_network	Run Seurat clustering
check_package	Check to ensure a package is installed
cluster_coords	Return embeddings coordinates from a given embedding name
cluster_multiome	Run multiome clustering
cluster_multiome2	Run multiome clustering
cluster_single_rna	Run Seurat clustering
convert_empty	Convert empty string to "-"
coverage_plot	ATAC coverage static plot
create_uploadinfo_object	create_uploadinfo_object
DefaultDimReduc	Find the default DimReduc
detect_delim	Automatically detect delimiters in a text file
disconnect_socketio	Disconnect socket-io server
echo_back	Echo back a message
example_cluster_coords	RAS
example_dr1	Run DR
example_dr_figure	Run DR peak-gene figure
example_gas	GAS
example_ras	RAS
example_ri_heatmap	Run RI heatmap
example_ri_heatmap2	Run RI heatmap
feature_coords	Return embeddings coordinates and feature expression
gene_cor_plot	Gene-gene correlation static plot
gene_umap_plot	Plot static gene UMAP
get_all_assays	Get all assays names from object
get_all_embeddings	Get all embedding/dimension reduction names from object
get_all_genes	Get all gene names/ids from object
get_all_idents	Get all Idents names from object
get_base_dir	Get base dir
getdata	Load dataset from "R" package using data(), assign it...
get_gene_range	Get genomic range of a gene and extend a flank region...
hello_name	Hello world function
ifnb_2800	Data of ifnb_2800
init_socketio	Disconnect socket-io server
interactive_heatmap	Interactive complex heatmap
iris3api-package	iris3api: IRIS3-api
is_matrix_empty	Check if a matrix is empty
list_regulon_network	Run Seurat clustering
load_citeseq	Load CITE-seq data
load_multiome	Load matched scRNA-seq and scATAC-seq data to Seurat / Signac
load_multiome2	Load matched scRNA-seq and scATAC-seq data to Seurat / Signac
load_multiome3	Load matched scRNA-seq and scATAC-seq data to Seurat / Signac
load_multiome4	Load matched scRNA-seq and scATAC-seq data to Seurat / Signac
load_multi_rna	Load multi scRNA-seq data to Seurat
load_single_rna	Load data to Seurat
log_request	Simple request logger
merge_idents	Merge active clusters
pipe	Pipe operator
plot_cellchat	Run CellChat
plot_enrichr_bar	Generate enrichment bar plot
plot_enrichr_dot	Generate enrichment dot plot
plot_gsea	Generate GSEA plot
plot_histogram	Plot a histogram of random numbers
print_wd	Print working directory and a message
read_deepmaps	Read file switcher
read_deepmaps_h5	Read 10x hdf5 format
read_deepmaps_text	Read csv,tsv,txt format
rename_idents	Rename clusters/idents
rna_qc_list	Get QC metrics list for single scRNA-seq dataset
rna_qc_plot	Variable genes scatter plot
run_cellchat	Run CellChat
select_category	Set or select category to assign labels
select_cells	Select cells based on criteria
send_progress	Send job progress to server
set_assay	Set Seurat Assay by name
set_embedding	Set embedding/dimension reduction by name
set_idents	Set Seurat Idents by name
set_if_not_null	Set a default value if an object is NOT null
set_if_null	Set a default value if an object is null
set_obj	Set subset obj or full_obj
start_debug_server	Start debug server
start_server	Start IRIS3 R api server
static_heatmap	Complex heatmap
style_and_lint	DEV tool: auto style and lint package
subset_cells	Select cells based on criteria
sum_numbers	Sum two numbers
umap_plot	Plot static UMAP
UploadInfo-class	Create UploadInfo object
violin_gene_plot	Plot violin gene UMAP
yan_2013	Data of yan_2013
zeisel_2015	Data of zeisel_2015