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Created with Raphaël 2.2.024Jan212019131176Dec15Nov12985229Oct251121Sep1716131Aug1913927Jul242221191716151413129876532129Jun2216141198312May107430Apr292323Mar19225Feb22179852127Jan25222120191815131275417Dec1627Nov2625242320191716629Oct28272625Sep24177Aug415Jul1063130Jun2625231918171210910Apr9627Mar26111096543Merge branch 'dev' of gitlab_lbmc:LBMC/regards/chia-pet_network into devget_project_colocalisation: script to find specific component signatures within communitiesget_project_colocalisation: creation of a file containing the matrix of the heatmapsrc/nt_composition/make_nt_correlation.py: add parameter experiment in get_project_colocalisation functionsrc/find_interaction_cluster/config.py: add output_std variablesrc/find_interaction_cluster/homogenous_frequencies_across_communities.py: script to discover community signaturesMerge branch 'dev' of gitbio.ens-lyon.fr:LBMC/regards/chia-pet_network into devsrc/db_utils/fill_EF_tables.py: add this script to add the cin_project_ef and cin_export_event tables to the databasesrc/find_interaction_cluster/Heatmap_composition/permutation.py: add agg parameter and p-value correctionsrc/find_interaction_cluster/Heatmap_composition/compo_heatmap.py: add parameter agg_funsrc/find_interaction_cluster/Heatmap_composition/frequency.py: in create_frequency_series add agg_fun parametersrc/find_interaction_cluster/homogenous_frequencies_across_communities.py: script that creates a figure showing the mean standard error of frequencies between each communities and a control of random featuresrc/find_interaction_cluster/community_figures/fig_functions.py: use corrected p-valuesrc/find_interaction_cluster/Heatmap_composition/permutation.py: use corrected p-valuesrc/find_interaction_cluster/radomization_test_ppi.py: add correction parametersrc/find_interaction_cluster/radomization_test_ppi.py: add correction parametersrc/find_interaction_cluster/nt_and_community.py: changes in the lmm statsrc/find_interaction_cluster/nt_and_community.py: major update to only be able to use a community file given in input rather than finding it thanks to many parameterssrc/find_interaction_cluster/config.py: add output_enrichment variable to ConfigGrand and change in get_community_file functionsrc/find_interaction_cluster/Heatmap_composition/compo_heatmap.py: change in generate_heatmap_matrix to be able to produce an heatmap using the mean average frequencies of nucleotides in every clusterssrc/find_interaction_cluster/Heatmap_composition/frequency.py: Add a parameter ref to the function create_frequency_seriessrc/find_interaction_cluster/Heatmap_composition/__main__.py: Mean_CMT can now be used as a value for the parameter --ctrlsrc/find_interaction_cluster/community_figures/fig_functions.py: change in make_barplot_perm to add a line corresponding to the mean of the average frequency of every clusterssrc/find_interaction_cluster/Heatmap_composition/frequency.py: fix create_frequency_series testsrc/find_interaction_cluster/__main__.py: commenting some functionsrc/find_interaction_cluster/community_calibration.py: add an experiment parameter on the main function make_calibrationsrc/find_interaction_cluster/create_community_size_distribution.py: set xlim between 0, 1000 in the figure produced by the function make_density_figuresrc/find_interaction_cluster/community_finder.py: add a parameter experiments in function multiple_community_launcher and other function that it callssrc/find_interaction_cluster/config.py: add experiment parameters on get_weight_folder and get_community_file functionssrc/find_interaction_cluster/clip_figures/get_similarities_between_communities.py: add two parameters ffor the function create_rand_index_heatmap to be able to compute similarity_indexsrc/find_interaction_cluster/clip_figures/communities_similarities.py: add a parameter method and similarity threshold to perform adjusted rand index computationsrc/find_interaction_cluster/clip_figures/my_rand_index.py: script that perform similarity index computation between two sets of communitiessrc/logging_conf.py: update logging confsrc/db_utils/__main__.py: don't fill exon tablesrc/db_utils/interactions/bedtools.py: don't perform analyzes on exonssrc/db_utils/hic_4DN_preprocessing/preprocessing_hic.py: main: add a parameter percentileMerge branch 'dev' of gitlab_lbmc:LBMC/regards/chia-pet_network into devsrc/find_interaction_cluster/create_community_size_distribution.py: creation of a script that aims to display the size distribution of communities in genes/exons numbersrc/figures_utils/tad_quality_control.py: script initiation to control hi-c and chia-pet datasets qualitysrc/figures_utils/config_figures.py: add variables to launch tad_quality_control.py script