Package index • HuMMuS

All functions

DefaultAssay() `DefaultAssay<-`(): Get Default assays of Hummus_Object (based on Seurat)

Hummus_Object-class Hummus_Object: The Hummus_Object class

Initiate_Hummus_Object(): Initiate a hummus object

VariableFeatures() `VariableFeatures<-`(): Variable features of assays in Hummus_Object (based on Seurat)

add_network(): Add a network to a multiplex, a multilayer or an hummus object

aggregate_matrix(): Aggregate matrix over groups

bipartite-class bipartite: Bipartite class

bipartite_peaks2genes(): Compute links between DNA regions and genenames

bipartite_tfs2peaks(): Compute links between TFs and DNA regions (ATAC peaks)

compute_atac_peak_network(): Compute peak network from scATAC-seq data

compute_gene_network(): Compute gene netwok from scRNA-seq data

compute_tf_network(): Compute TF network and add it to hummus object

dMcast(): Copy of the dMcast function from the Matrix.utils package, since this is off CRAN and does not seem to be maintained anymore internally

define_binding_regions(): Define binding_regions from hummus object

define_enhancers(): Define enhancers from hummus object

define_general_config(): Define general config file for hummuspy

define_grn(): Define GRN from hummus object

define_output(): Define output from hummus object

define_target_genes(): Define target genes from hummus object

fast_aggregate(): Copy of the aggregate.Matrix function from the Matrix.utils package, since this is off CRAN and does not seem to be maintained anymore internally

find_peaks_near_genes(): Associate peaks to genes based on distance to TSS (or gene body)

format_bipartites_names(): Format bipartites names for python hummuspy package config functions

format_multiplex_names(): Format multiplex names for python hummuspy package config functions

get_genome_annotations(): Fetch online genome annotations from Ensembldb database

get_tf2motifs(): Fetch online TF motifs from JASPAR2020 and chromVARmotifs

get_tfs(): Extract TF names from scRNA data and tf2motifs

motifs_db-class motifs_db: Motifs database class

multilayer-class multilayer: Multilayer class

multiplex-class multiplex: Multiplex class

peaks_in_regulatory_elements(): Filter peaks to those overlapping specific (regulatory) elements

run_cicero_wrapper(): Cicero wrapper function for the compute_atac_peak_network function

run_tf_null_wrapper(): tf_null wrapper function for the tf_network function

save_multilayer(): Save multilayer object files in a hierarchical structure on disk

store_network(): Wrapper function to save a network or not

`[[`(<Hummus_Object>): Access assays in Hummus_Object (based on Seurat)