GitHub - KellisLab/EPIMAP_ANALYSIS: Epimap processing and analysis code repository

Epimap Analysis code repository

Epimap (Epigenome Integration across Multiple Annotation Projects) downloading, processing, ChromHMM/ChromImpute, clustering, and all subsequent analysis code.

Contact: cboix at mit

Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
ChromImpute_SRC		ChromImpute_SRC
epimapAUX		epimapAUX
great_enrichment		great_enrichment
gwas_enrichment		gwas_enrichment
meme_enrichment		meme_enrichment
snake_pipe		snake_pipe
.gitignore		.gitignore
.tmp		.tmp
BAMtoTA_download_preprocess.sh		BAMtoTA_download_preprocess.sh
Call_peaks.sh		Call_peaks.sh
ChIP_pipeline.sh		ChIP_pipeline.sh
Generate_signal_tracks.sh		Generate_signal_tracks.sh
Pool_subsample_SCCA.sh		Pool_subsample_SCCA.sh
README.md		README.md
addRank2NarrowPeakFile.sh		addRank2NarrowPeakFile.sh
aggregate_binary_txt_to_npy.py		aggregate_binary_txt_to_npy.py
altindex_auxfunctions.R		altindex_auxfunctions.R
altindex_build_list.R		altindex_build_list.R
altindex_mergepks.sh		altindex_mergepks.sh
auxfunc_masterlist.py		auxfunc_masterlist.py
auxfunc_masterlist.pyc		auxfunc_masterlist.pyc
auxiliary_chromImpute_functions.R		auxiliary_chromImpute_functions.R
auxiliary_function_general_repel.R		auxiliary_function_general_repel.R
auxiliary_gwastree_functions.R		auxiliary_gwastree_functions.R
auxiliary_gwastree_plotting_functions.R		auxiliary_gwastree_plotting_functions.R
bedgraph_compress.sh		bedgraph_compress.sh
by_header.awk		by_header.awk
calculate_all_flat_enrichments.R		calculate_all_flat_enrichments.R
calculate_all_gwastree_enrichments.R		calculate_all_gwastree_enrichments.R
calculate_diff_of_datasets.py		calculate_diff_of_datasets.py
calculate_distance_of_datasets.py		calculate_distance_of_datasets.py
calculate_observed_emissions_overlap_chmm.R		calculate_observed_emissions_overlap_chmm.R
calculate_permuted_flat_enrichments.R		calculate_permuted_flat_enrichments.R
calculate_permuted_gwastree_enrichments.R		calculate_permuted_gwastree_enrichments.R
calculate_unexpected_genes_modules.R		calculate_unexpected_genes_modules.R
callpeak_from_imputedbw.sh		callpeak_from_imputedbw.sh
catch_rerun.sh		catch_rerun.sh
check_ChromImpute.sh		check_ChromImpute.sh
check_procfiles.sh		check_procfiles.sh
choose_expression_files.R		choose_expression_files.R
choose_rand_regions.R		choose_rand_regions.R
chunk_bed.awk		chunk_bed.awk
clean_procfiles.sh		clean_procfiles.sh
cluster_binary_mat.py		cluster_binary_mat.py
collate_chromimpute_distance.sh		collate_chromimpute_distance.sh
collate_expression_tsv.sh		collate_expression_tsv.sh
compile_plot_eval_metrics.sh		compile_plot_eval_metrics.sh
compress_bw_to_hd5py.py		compress_bw_to_hd5py.py
compute_coverage_overall_chromHMM.sh		compute_coverage_overall_chromHMM.sh
config_ChromImpute.sh		config_ChromImpute.sh
count_snps_tree.R		count_snps_tree.R
count_unique_enriched_snps.R		count_unique_enriched_snps.R
create_chmm_state_possiblelist.py		create_chmm_state_possiblelist.py
create_gwas_intersect_matrix.sh		create_gwas_intersect_matrix.sh
create_permuted_catalogs.R		create_permuted_catalogs.R
determine_resampling_performance.sh		determine_resampling_performance.sh
distance_between_binned.sh		distance_between_binned.sh
distance_from_contingency.R		distance_from_contingency.R
explore_gwastree_methodology.R		explore_gwastree_methodology.R
extract_allbw_region.sh		extract_allbw_region.sh
extract_bw_bins.R		extract_bw_bins.R
extract_bw_on_peaks.sh		extract_bw_on_peaks.sh
extract_plot_chromHMM_region.sh		extract_plot_chromHMM_region.sh
extract_signaldistr_statespecific.py		extract_signaldistr_statespecific.py
general_EPIMAP_ANALYSIS.R		general_EPIMAP_ANALYSIS.R
get_RNAseq_microarray_ENCODE.R		get_RNAseq_microarray_ENCODE.R
get_available_ENCODE_links.R		get_available_ENCODE_links.R
get_experiments_ENCODE.R		get_experiments_ENCODE.R
get_mappability_tracks.sh		get_mappability_tracks.sh
get_metadata_ENCODE.R		get_metadata_ENCODE.R
get_roadmap_enh.sh		get_roadmap_enh.sh
get_roadmap_mapping.R		get_roadmap_mapping.R
install_processing_dependencies.sh		install_processing_dependencies.sh
intersect_gwas_with_index.sh		intersect_gwas_with_index.sh
load_distance_matrices.R		load_distance_matrices.R
load_gwastree_analysis.R		load_gwastree_analysis.R
load_metadata.R		load_metadata.R
load_modules_data.R		load_modules_data.R
load_region_distance_matrices.R		load_region_distance_matrices.R
load_statistics_gwastree_enrichments.R		load_statistics_gwastree_enrichments.R
load_validation_gwastree_enrichments.R		load_validation_gwastree_enrichments.R
make_and_transfer_bw_for_release.sh		make_and_transfer_bw_for_release.sh
make_bw_for_release.sh		make_bw_for_release.sh
make_contingency_table_for_binned.sh		make_contingency_table_for_binned.sh
make_impobs_tables.sh		make_impobs_tables.sh
make_uniform_control.sh		make_uniform_control.sh
metrics_resampled_data.sh		metrics_resampled_data.sh
munge_CAD_example_sumstats.sh		munge_CAD_example_sumstats.sh
parse_config.py		parse_config.py
parse_config.pyc		parse_config.pyc
plot_CAD_example_analysis.R		plot_CAD_example_analysis.R
plot_CAD_sumstats_qqplots.R		plot_CAD_sumstats_qqplots.R
plot_aggregate_stats_bwpk.R		plot_aggregate_stats_bwpk.R
plot_all_gwastree_example_analysis.R		plot_all_gwastree_example_analysis.R
plot_chromHMM_frequencies.R		plot_chromHMM_frequencies.R
plot_chromHMM_region.R		plot_chromHMM_region.R
plot_chromImpute_diff_qc.R		plot_chromImpute_diff_qc.R
plot_chromImpute_distance.R		plot_chromImpute_distance.R
plot_chromImpute_imputed_distance.R		plot_chromImpute_imputed_distance.R
plot_chromImpute_imputed_trees.R		plot_chromImpute_imputed_trees.R

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