annotation_from_merged_peaks	annotation_from_merged_peaks
annotToCol2	annotToCol2
anocol_binary	anocol_binary
anocol_categorical	anocol_categorical
bams_to_matrix_indexes	bams_to_matrix_indexes
beds_to_matrix_indexes	beds_to_matrix_indexes
calculate_CNA	calculate_CNA
calculate_cyto_mat	calculate_cyto_mat
calculate_gain_or_loss	calculate_gain_or_loss
calculate_logRatio_CNA	calculate_logRatio_CNA
call_macs2_merge_peaks	call_macs2_merge_peaks
changeRange	changeRange
CheA3_TF_nTargets	CheA3_TF_nTargets
check_correct_datamatrix	check_correct_datamatrix
choose_cluster_scExp	choose_cluster_scExp
choose_perplexity	choose_perplexity
col2hex	col2hex
colors_scExp	colors_scExp
combine_datamatrix	combine_datamatrix
combine_enrichmentTests	combine_enrichmentTests
comparable_variables	comparable_variables
CompareedgeRGLM	CompareedgeRGLM
CompareWilcox	CompareWilcox
concatenate_scBed_into_clusters	concatenate_scBed_into_clusters
consensus_clustering_scExp	consensus_clustering_scExp
correlation_and_hierarchical_clust_scExp	correlation_and_hierarchical_clust_scExp
count_coverage	count_coverage
create_project_folder	create_project_folder
create_sample_name_mat	create_sample_name_mat
create_scDataset_raw	create_scDataset_raw
create_scExp	create_scExp
DA_custom	DA_custom
DA_one_vs_rest	DA_one_vs_rest
DA_pairwise	DA_pairwise
define_feature	define_feature
detect_samples	detect_samples
differential_activation	differential_activation
differential_analysis_scExp	differential_analysis_scExp
distPearson	distPearson
enrichmentTest	enrichmentTest
enrich_TF_ChEA3_genes	enrich_TF_ChEA3_genes
enrich_TF_ChEA3_scExp	enrich_TF_ChEA3_scExp
exclude_features_scExp	exclude_features_scExp
feature_annotation_scExp	feature_annotation_scExp
filter_correlated_cell_scExp	filter_correlated_cell_scExp
filter_genes_with_refined_peak_annotation	filter_genes_with_refined_peak_annotation
filter_scExp	filter_scExp
find_clusters_louvain_scExp	find_clusters_louvain_scExp
find_top_features	find_top_features
generate_analysis	generate_analysis
generate_count_matrix	generate_count_matrix
generate_coverage_tracks	generate_coverage_tracks
generate_feature_names	generate_feature_names
generate_report	generate_report
gene_set_enrichment_analysis_scExp	gene_set_enrichment_analysis_scExp
getExperimentNames	getExperimentNames
getMainExperiment	getMainExperiment
get_color_dataframe_from_input	get_color_dataframe_from_input
get_cyto_features	get_cyto_features
get_genomic_coordinates	get_genomic_coordinates
get_most_variable_cyto	get_most_variable_cyto
get_pathway_mat_scExp	get_pathway_mat_scExp
gg_fill_hue	gg_fill_hue
groupMat	groupMat
H1proportion	H1proportion
has_genomic_coordinates	has_genomic_coordinates
hclustAnnotHeatmapPlot	hclustAnnotHeatmapPlot
hg38.chromosomes	hg38.chromosomes
hg38.cytoBand	hg38.cytoBand
hg38.GeneTSS	hg38.GeneTSS
imageCol	imageCol
import_count_input_files	import_count_input_files
import_scExp	import_scExp
index_peaks_barcodes_to_matrix_indexes	index_peaks_barcodes_to_matrix_indexes
inter_correlation_scExp	inter_correlation_scExp
intra_correlation_scExp	intra_correlation_scExp
launchApp	launchApp
load_MSIGdb	load_MSIGdb
merge_MACS2_peaks	merge_MACS2_peaks
mm10.chromosomes	mm10.chromosomes
mm10.cytoBand	mm10.cytoBand
mm10.GeneTSS	mm10.GeneTSS
normalize_scExp	normalize_scExp
num_cell_after_cor_filt_scExp	num_cell_after_cor_filt_scExp
num_cell_after_QC_filt_scExp	num_cell_after_QC_filt_scExp
num_cell_before_cor_filt_scExp	num_cell_before_cor_filt_scExp
num_cell_in_cluster_scExp	num_cell_in_cluster_scExp
num_cell_scExp	num_cell_scExp
pca_irlba_for_sparseMatrix	pca_irlba_for_sparseMatrix
plot_cluster_consensus_scExp	plot_cluster_consensus_scExp
plot_correlation_PCA_scExp	plot_correlation_PCA_scExp
plot_coverage_BigWig	plot_coverage_BigWig
plot_differential_summary_scExp	plot_differential_summary_scExp
plot_differential_volcano_scExp	plot_differential_volcano_scExp
plot_distribution_scExp	plot_distribution_scExp
plot_gain_or_loss_barplots	plot_gain_or_loss_barplots
plot_heatmap_scExp	plot_heatmap_scExp
plot_inter_correlation_scExp	plot_inter_correlation_scExp
plot_intra_correlation_scExp	plot_intra_correlation_scExp
plot_most_contributing_features	plot_most_contributing_features
plot_percent_active_feature_scExp	plot_percent_active_feature_scExp
plot_pie_most_contributing_chr	plot_pie_most_contributing_chr
plot_reduced_dim_scExp	plot_reduced_dim_scExp
plot_reduced_dim_scExp_CNA	plot_reduced_dim_scExp_CNA
plot_top_TF_scExp	plot_top_TF_scExp
plot_violin_feature_scExp	plot_violin_feature_scExp
preprocessing_filtering_and_reduction	preprocessing_filtering_and_reduction
preprocess_CPM	preprocess_CPM
preprocess_feature_size_only	preprocess_feature_size_only
preprocess_RPKM	preprocess_RPKM
preprocess_TFIDF	preprocess_TFIDF
preprocess_TPM	preprocess_TPM
rawfile_ToBigWig	rawfile_ToBigWig
raw_counts_to_sparse_matrix	raw_counts_to_sparse_matrix
read_count_mat_with_separated_chr_start_end	read_count_mat_with_separated_chr_start_end
read_sparse_matrix	read_sparse_matrix
rebin_helper	rebin_helper
rebin_matrix	rebin_matrix
reduce_dims_scExp	reduce_dims_scExp
reduce_dim_batch_correction	reduce_dim_batch_correction
remove_chr_M_fun	remove_chr_M_fun
remove_non_canonical_fun	remove_non_canonical_fun
results_enrichmentTest	results_enrichmentTest
retrieve_top_bot_features_pca	retrieve_top_bot_features_pca
run_pairwise_tests	run_pairwise_tests
run_tsne_scExp	run_tsne_scExp
scExp	scExp
separate_BAM_into_clusters	separate_BAM_into_clusters
separator_count_mat	separator_count_mat
smoothBin	smoothBin
subsample_scExp	subsample_scExp
subset_bam_call_peaks	subset_bam_call_peaks
summary_DA	summary_DA
swapAltExp_sameColData	swapAltExp_sameColData
table_enriched_genes_scExp	table_enriched_genes_scExp
warning_DA	warning_DA
warning_filter_correlated_cell_scExp	warning_filter_correlated_cell_scExp
warning_plot_reduced_dim_scExp	warning_plot_reduced_dim_scExp
warning_raw_counts_to_sparse_matrix	warning_raw_counts_to_sparse_matrix
wrapper_Signac_FeatureMatrix	wrapper_Signac_FeatureMatrix
