Files in pcahan1/epoch
Dynamic GRN reconstruction from single cell RNA-Seq data
.DS_Store
DESCRIPTION
LICENSE
NAMESPACE
R/.DS_Store
R/.Rapp.history
R/0_utils.R
R/1_GRN.R
R/2_crossweighting.R
R/3_dynamicGRN.R
R/4_plotting.R
R/5_networkComparison.R
R/6_networkAnalysis.R
README.md
data/.DS_Store
data/effectortargets_mouse.rda
data/example1_dyanmicGRN.rda
data/example1_epochs.rda
data/example1_net.rda
data/example2_epochs2.rda
data/example2_net2.rda
data/hsTFs.rda
data/mmTFs.rda
data/mouse_signaling_binding/FGF-MAPK_Etv5.1.tsv
data/mouse_signaling_binding/FGF-PI3K_Foxo1.1.tsv
data/mouse_signaling_binding/FGF-STAT_Stat3.1.tsv
data/mouse_signaling_binding/FGF-STAT_Stat5a.1.tsv
data/mouse_signaling_binding/FGF-STAT_Stat5b.1.tsv
data/mouse_signaling_binding/HH_Gli1.1.tsv
data/mouse_signaling_binding/HH_Gli2.1.tsv
data/mouse_signaling_binding/HH_Gli3.1.tsv
data/mouse_signaling_binding/HIPPO_Yap1.1.tsv
data/mouse_signaling_binding/NOTCH_Rbpj.1.tsv
data/mouse_signaling_binding/TGFb-ACT_Smad2.1.tsv
data/mouse_signaling_binding/TGFb-ACT_Smad3.1.tsv
data/mouse_signaling_binding/TGFb-BMP_Smad1.1.tsv
data/mouse_signaling_binding/TGFb_Smad4.1.tsv
data/mouse_signaling_binding/WNT_Ctnnb1.1.tsv
data/mouse_signaling_binding/WNT_Lef1.1.tsv
data/mouse_signaling_binding/WNT_Tcf7.1.tsv
data/mouse_signaling_binding/WNT_Tcf7l2.1.tsv
data/sampled_mesoderm_WAG.loom
img/.DS_Store
img/example1_heatmapTFs.png
img/example1_regulatorsoftargets.png
img/example1_topregulators.png
img/example2_network1_on.png
img/example3_WNT_heatmap.png
man/JI_across_topregs.Rd
man/add_interaction_type.Rd
man/add_type.Rd
man/assign_epochs.Rd
man/assign_epochs_simple.Rd
man/biglist_compute_betweenness_degree.Rd
man/caoGenes.Rd
man/cn_extractRegsDF.Rd
man/compileDynGenes.Rd
man/compile_epochs.Rd
man/compute_JI_topregs.Rd
man/compute_betweenness_degree.Rd
man/compute_frobenius_distance.Rd
man/compute_pagerank.Rd
man/cor_and_add_action.Rd
man/crossweight.Rd
man/define_epochs.Rd
man/diffnet_community_detection.Rd
man/dynamic_difference_network.Rd
man/dynamic_shortest_path.Rd
man/dynamic_shortest_path_multiple.Rd
man/edge_rank.Rd
man/edge_uniqueness.Rd
man/epochGRN.Rd
man/findDynGenes.Rd
man/find_communities.Rd
man/find_cuts_by_clustering.Rd
man/find_cuts_by_similarity.Rd
man/find_targets.Rd
man/grnKsmooth.Rd
man/heatmap_by_treatment_group.Rd
man/hm_dyn.Rd
man/hm_dyn_clust.Rd
man/hm_dyn_epoch.Rd
man/ig_tabToIgraph.Rd
man/loadDataFromLoom.Rd
man/load_SP_effectors.Rd
man/mean_module_expression.Rd
man/mean_subnetwork_expression.Rd
man/order_genes.Rd
man/plot_diffnet_detail.Rd
man/plot_dyn_diffnet.Rd
man/plot_dynamic_network.Rd
man/plot_dynnet_detail.Rd
man/plot_heatmap_by_treatment.Rd
man/plot_targets.Rd
man/plot_targets_and_regulators.Rd
man/plot_targets_with_top_regulators.Rd
man/plot_targets_with_top_regulators_detail.Rd
man/plot_top_regulators.Rd
man/reconstructGRN.Rd
man/reconstructGRN_GENIE3.Rd
man/sample_and_epoch_reconstruct.Rd
man/score_targets.Rd
man/split_epochs_by_group.Rd
man/split_epochs_by_pseudotime.Rd
man/static_shortest_path.Rd
man/subnets.Rd
man/tfnet_pagerank.Rd
man/utils_loadObject.Rd
man/wn_ig_tabToIgraph.Rd
vignettes/mESC_GRN_reconstruction.md
