API for shmohammadi86/ATACtion
ATACtion is the ACTIONet extension for sc/sn-ATAC-seq data analysis

Global functions
ATACtion Man page
GI.to.peakConnectivity.mat Source code
GenomicInteractions.to.cicero Source code
add.binarized.counts Source code
add_motif_matched_to_ATACtion Source code
add_physical_peak_gene_interactions_to_ATACtion Source code
add_proximal_peak_gene_interactions_to_ATACtion Source code
annotate.GR.peaks Source code
annotate_ATACTion_peaks Source code
annotate_ATACtion_cells_using_markers Source code
cicero.to.GenomicInteractions Source code
compute_ATAC_archetype_to_ATAC_archetype_alignment Source code
compute_ATAC_archetype_to_RNA_archetype_alignment Source code
compute_ATAC_cell_to_ATAC_cell_alignment Source code
compute_ATAC_cell_to_RNA_cell_alignment Source code
compute_ATACtion_archSE Source code
compute_GRList_enrichment_from_ATACtion Source code
compute_RNA_archetype_to_ATAC_archetype_alignment Source code
compute_RNA_cell_to_ATAC_cell_alignment Source code
compute_TF_enrichment_from_ATACtion Source code
compute_bulkATAC_to_ATAC_archetype_alignment Source code
compute_bulkRNA_to_ATAC_archetype_alignment Source code
compute_cicero_ccans Source code
compute_cicero_gene_expression Source code
compute_gene_enrichment_from_ATACtion Source code
compute_geneset_enrichment_from_ATACtion Source code
conn.to.peakConnectivity.mat Source code
export_ATACtion_to_SnapATAC Source code
export_ATACtion_to_cisTopic Source code
extend.cisConnectome.usingConns Source code
extend.cisConnectome.usingGI Source code
extract_SnapATAC_reduction Source code
extract_cisTopic_factors Source code
get_ATACtion_enrichment Source code
import_ATACtion_from_10X Source code
import_ATACtion_from_ArchR Source code
import_ATACtion_from_SnapATAC Source code
impute_TF_activity_using_ATACtion Source code
impute_gene_expression_using_ATACtion Source code
impute_genome_wide_activity Source code
impute_genomewide_ATAC_signals Source code
insertionProfileSingles Source code
insertionProfileSingles_helper Source code
is.GR Source code
liftOverGR Source code Source code
liftOverGR_list Source code Source code
load_gwascat_GR Source code
plot_ATACtion_TF_view Source code
plot_ATACtion_gene_view Source code
plot_archetype_tracks Source code
project_ATACtion_enrichment_to_cells Source code
reduceChromatinAccessibility Source code
reduce_peaks_using_ACTION Source code
reduce_peaks_using_LSACTION Source code
reduce_peaks_using_LSI Source code
reduce_peaks_using_chromVAR Source code
run_ATACtion Source code
run_ATACtion_cicerify Source code
run_SnapATAC Source code
run_cisTopic Source code
tabulate2dCpp Source code
visualize_marker_genes_over_ATACtion Source code
shmohammadi86/ATACtion documentation built on June 13, 2021, 3:18 a.m.