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Created with Raphaël 2.2.012Jul9876532129Jun2216141198312May107430Apr292323Mar19225Feb22179852127Jan25222120191815131275417Dec1627Nov2625242320191716629Oct28272625Sep24177Aug415Jul1063130Jun2625231918171210910Apr9627Mar26111096543Update create_table_4_community_figures.pymodified: src/visualize_comunities/fig_functions.pysrc/find_interaction_cluster/community_figures/create_table_4_community_figures.py: fix filter step to have all genes in the studied tablesrc/generate_DE_list_for_interaction_analysischanged path nt_analysis and changed peak desity columnchecking src/find_interaction_cluster/clip_figures/clip_compo_analyser.py with Nicolas 2checking src/find_interaction_cluster/clip_figures/clip_compo_analyser.py with Nicolasfixed heatmap and barplots pathsadded plotly heatmap and eliminated impoverishedchanged heatmap colors , added the 'simple-reg' filteringupdataed src/automation/execute_PSMN.shupdated execute_PSMN.shadd PSMN_execute.shfirst commit added my stagedsrc/find_interaction_cluster/heatmap_cluster.py: perform a composition bias analysis on the genes located inside the most enriched/impoverished spatial clusters in genes regulated by a factor + add the gene names in json filessrc/find_interaction_cluster/config.py: add enrichment module variablesrc/find_interaction_cluster/barplot_factor_n_enriched_clusters.py: barplot are now sorted by the number of up or down regulated features for each factorsrc/find_interaction_cluster/heatmap_cluster.py: add the creation of json file and violin figure to study the number of feature (gene/exon) localised in clusters of spatial communities or in cluster of factorssrc/find_interaction_cluster/config.py: add a parameter clustering with the value 'complete'src/find_interaction_cluster/heatmap_cluster.py: add a parameter to create heatmap based on p-valuesrc/find_interaction_cluster/community_figures/fig_functions.py: add a new column simple-regsrc/find_interaction_cluster/heatmap_cluster.py: fix call to get_heatmap_table in heatmap_creator functionsrc/find_interaction_cluster/heatmap_cluster.py: add a parameter to selected the factor displayed on the figure based on the number of feature regulated by this factorsrc/figures_utils/TF_venn_of_project_with_common_origin.py: figure to create venn diagram between projects of the same originmastermastersrc/figures_utils/config_figures.py: add a new variable venn_tfsrc/db_utils/fill_TF_tables.py: major changes to parse knockTF variablessrc/db_utils/config.py: change of three variables and add new knocktf variablessrc/db_utils/db_creation.py: modification of create_cin_project_tf_table function to add a new column : knock_methodsrc/find_interaction_cluster/clip_figures/clip_analyser.py: change in create_table to be able to select the kind offactor to analysesrc/find_interaction_cluster/barplot_factor_n_enriched_clusters.py: Script that creates barplots figures for every splicing factor indicating how many genes are up and down regulated by every splicing factor and the number of spatial cluster enriched in those genessrc/find_interaction_cluster/config.py: add a variable output_barplotssrc/find_interaction_cluster/clip_figures/clip_analyser.py: update testssrc/find_interaction_cluster/heatmap_cluster.py: print more detailssrc/find_interaction_cluster/heatmap_cluster.py: create heatmap of the percentage of regulated features for each factors in each communitysrc/find_interaction_cluster/config.py: add a variable output heatmapsrc/find_interaction_cluster/sf_and_community_recap_table.py: creates a recap table of the results produced by sf_and_other_communitities.pysrc/find_interaction_cluster/sf_and_other_communitities.py: script to check if splicing or transcription factors regulates genes/exons concentrated in communities for 7 community filessrc/find_interaction_cluster/__main__.py: launch community enrichment for genes regulated by splicing factors and transcription factorssrc/find_interaction_cluster/config.py: add output_factor variablesrc/find_interaction_cluster/sf_and_communities.py: fixes and modification to create one file for each regulation and. modification to handle transcription factors