src/download_encode_eclip/merge_eclip.py: add a parameter level in create_merged_files function to filter within genes (without first and last exons) or within exons (extended by 200 nt at each side)

src/download_encode_eclip/create_gene_bed.py: add a parameter level in create_gene_bed to choose ti create a bed containing genes without their first and last exons or a bed file containing exons (extended by 200 nt at both side) without the first and the last exons

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/download_encode_eclip/merge_eclip.py: modification of merge_files function to filter onily the peaks with a score of 1000 and inside a gene (first and last exons not included)"

src/download_encode_eclip/create_gene_bed.py: script to create a bed file of human geneswithout the first and the last exons

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/download_encode_eclip/merge_eclip.py: modification of merge_files function to remove the heading chr in the first bed column

src/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: Add a step that merges the TADs before the liftover

src/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: change in liftover and check_n_save_bed function

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/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