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Created with Raphaël 2.2.013Aug927Jul242221191716151413129876532129Jun2216141198312May107430Apr292323Mar19225Feb22179852127Jan25222120191815131275417Dec1627Nov2625242320191716629Oct28272625Sep24177Aug415Jul1063130Jun2625231918171210910Apr9627Mar26111096543src/find_interaction_cluster/Go_annotation/__main__.py: add min_level parametersrc/find_interaction_cluster/Go_annotation/create_go_communities.py: change to be able to remove generic go termsrc/find_interaction_cluster/Go_annotation/download_go_files.py: add functions to find the level of each go term from the root termsrc/find_interaction_cluster/Go_annotation/config_go.py: add a dictionary go_rootsrc/find_interaction_cluster/Heatmap_composition/compo_heatmap.py: fix Heatmap_composrc/find_interaction_cluster/Go_annotation/__main__.py: add parameter thresholdsrc/find_interaction_cluster/Go_annotation/create_go_communities.py: filter bi communitiessrc/find_interaction_cluster/Heatmap_composition/compo_heatmap.py: fix create_community_filesrc/find_interaction_cluster/Heatmap_composition/__main__.py: modification of the com_file parametersrc/find_interaction_cluster/Heatmap_composition/compo_heatmap.py: modification of the com_file parameters to be able to create composition heatmp for splicing factors and transcription factorssrc/find_interaction_cluster/Heatmap_composition/__main__.py: add parameter htypesrc/find_interaction_cluster/Heatmap_composition/compo_heatmap.py: add a parameter htype for generate_heatmap_matrix functionsrc/find_interaction_cluster/Heatmap_composition/frequency.py: add function create_frequency_seriessrc/find_interaction_cluster/Heatmap_composition/permutation.py: change in randomization_test_maker functionsrc/find_interaction_cluster/Heatmap_composition/*.py: add script that allows the creation of composition Heatmapssrc/find_interaction_cluster/Go_annotation/*.py: add a submodule to create community files that cluster the gene by their finest GO termfixed down and up reversed problem in combined violin 2fixed down and up reversed problem in combined violinadded src/automation/execute_composition_heatmap.sh and checked resultsadded module src/find_interaction_cluster/composition_heatmap.py to create composition heatmaps v.0fixed filtering .bed in heatmapsadded merging violin plots optionfiltered the heatmap table to only show TF with DE>200 and at least one enriched communties for both up and downadded src/find_interaction_cluster/clip_figures/vis_comp_recap.pyadded direct_comp 2added direct_compfast_comp 2fast_compadded communities files paths to clip_figures/Config //fixing heatmap errorfixedfixed shiny interactive plots and added all_DE filter to count_DE_genesadded unilateral-test nicolas changeseliminated peack density from titlesrc/find_interaction_cluster/heatmap_cluster.py: add alternative parametersrc/find_interaction_cluster/community_figures/{__main__.py, fig_functions.py}: add alternative parametersrc/find_interaction_cluster/radomization_test_ppi.py: add parameter alternative to get_pvalue functionMerge branch 'Ali_branch' of gitbio.ens-lyon.fr:LBMC/regards/chia-pet_network into Ali_branch added src/automation/composition.shUpdate create_table_4_community_figures.pymodified: src/visualize_comunities/fig_functions.py