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/hic_TAD_caller/create_TAD_HiC_files/__main__.py: creation of a function launcher with a parameter resolution

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/hic_TAD_caller/: Script to call TADs with ArrowHead from different Hic files recovered from data.4dnucleome.org

src/nt_composition/config.py src/nt_composition/distance.py src/nt_composition/make_nt_correlation.py: change the calls of get_good_project

src/figures_utils/config_figures.py: add a parameter to get_good_project to select the cell of interest in our projects

src/download_encode_eclip/get_encode_clips.py: modifications to be hable to download  RIP-seq, iCLIP and RIP-chip experiments

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/download_encode_eclip/*.py: creation of a module used to download all the eclip data (on hg19) from Encode

src/misc/: script that creates a table indicating the number of splicing lore, chia-pet and clip project made on each cell line

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