src/find_interaction_cluster/clip_figures/clip_compo_analyser.py: changes to be able to use an expression file to filter out unexpressed genes

src/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: changes in select_community_file, create_figure function and creation of load_clip_folder_param function: allow to create community figure showing enrichement for gene/exon regulated (in splicing) by a splicing factor

src/find_interaction_cluster/clip_figures/clip_analyser.py: add new functions get_ctrl_exon get_regulation_table and modification of create_table function to be able to make community figure based on exon/gene regulated in splicing by a splicing factor

src/find_interaction_cluster/clip_figures/clip_analyser_fake_community.py: script to create fake community based on the peak density of each genes

src/find_interaction_cluster/clip_figures/communities_similarities.py: Create the adjusted rand index heatmap of the differnts communities

src/find_interaction_cluster/clip_figures/clip_compo_analyser.py: the differents violins (enriched, imoverished) are now order in the figure with custom colors

src/find_interaction_cluster/clip_figures/clip_compo_analyser.py: chnages and creation of new functions

creation of function to handle clip results folder produced by clip_launcher_4_many_communities and modification of get_middle_group, get_extreme_groups and get_interest_groups to simplify the names of each groups + pep8 chnages

src/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: chnage tiles in merge_figures function + pep8 changes

src/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: add pointsize argument in mantage command

src/find_interaction_cluster/tad_to_communities/tad_to_communities.py: creation of functions targeted_tad_to_communities removing_chr and targeted_bedtools_intersect to convert custom TAD to communities

src/find_interaction_cluster/config.py: fix merge problem by re-creating function get_communities_basefile

src/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: create for each clip the community figures obtained using many community files

src/find_interaction_cluster/clip_figures/config.py: add variables communities and communitites name

src/find_interaction_cluster/__main__.py src/find_interaction_cluster/community_finder.py: add the parameter use weight

src/find_interaction_cluster/community_calibration.py: creation of input and output for hipMCL inside it's result folder

src/find_interaction_cluster/clip_figures/__main__.py src/find_interaction_cluster/clip_figures/clip_analyser.py: ad dinflation parameter

src/find_interaction_cluster/community_finder.py: add inflation parameter to multiple_community_launcher function

src/find_interaction_cluster/*.py: add a parameter inflation in get_community_file function broadly use in this submodule

src/find_interaction_cluster/community_calibration.py: create a script to see the variation of modularity when the inflation parameter changes

src/find_interaction_cluster/community_finder.py: fix create_graph to use weight if wanted + add 2 paramters in findo_community functions

src/find_interaction_cluster/clip_figures/clip_analyser.py: change in add_regulation_column to display if the gene contains an exons regulated by a splicing factor rather than the proportion of regulated exon inside each gene

src/find_interaction_cluster/community_figures/fig_functions.py: change in lm_maker_summary function to avoid creation of a temp file

src/find_interaction_cluster/community_figures/fig_functions.py: change de offset between community_size and community_data axis

src/find_interaction_cluster/clip_figures/clip_analyser.py: deletion of files=[files[0]] in clip_folder_analysis function

src/find_interaction_cluster/community_figures/fig_functions.py: handles community_data column + fix logit test