Code for NIEB conservation analysis

Code there is used for NIEB conservation analysis.

Snakefile list the commands used.

You might need to add a bunch of stuff and sort files in the right folders for them to work. Sorry!

Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
biotools @ 993d2b5		biotools @ 993d2b5
envs		envs
.gitignore		.gitignore
.gitmodules		.gitmodules
CMakeLists.txt		CMakeLists.txt
Readme.md		Readme.md
Snakefile		Snakefile
agg_block_chain.py		agg_block_chain.py
bedToAOE.R		bedToAOE.R
collect_random_matrices.R		collect_random_matrices.R
compute_distribution.R		compute_distribution.R
createWindowNoOverlap.py		createWindowNoOverlap.py
create_contingency_table.R		create_contingency_table.R
create_matrix.R		create_matrix.R
deduplicate_blocks.R		deduplicate_blocks.R
extractGapsBlocks.py		extractGapsBlocks.py
filter_files.R		filter_files.R
fit_gc_windows.R		fit_gc_windows.R
get_gc_for_multiple_identical_ids.py		get_gc_for_multiple_identical_ids.py
get_gc_id.py		get_gc_id.py
get_sd_chains.R		get_sd_chains.R
get_sd_chains_split.R		get_sd_chains_split.R
intersect_reassembled.py		intersect_reassembled.py
make_unique_ids.py		make_unique_ids.py
merge_chains_back.R		merge_chains_back.R
merge_infos_chains.R		merge_infos_chains.R
merge_infos_chains_gaps.R		merge_infos_chains_gaps.R
plot_density.R		plot_density.R
plot_gc_corrected_density.R		plot_gc_corrected_density.R
plot_gc_corrected_gaps.R		plot_gc_corrected_gaps.R
plot_gc_nieb_window.R		plot_gc_nieb_window.R
plot_heatmap_cover_block.R		plot_heatmap_cover_block.R
plot_heatmap_cover_size.R		plot_heatmap_cover_size.R
plot_signal.R		plot_signal.R
select_best_ids.R		select_best_ids.R
select_sd_chains.R		select_sd_chains.R
split_chains_and_attribute_ids.py		split_chains_and_attribute_ids.py

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