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ChromImpute_SRC
ChromImpute_SRC
 
 
altindex_scripts
altindex_scripts
 
 
cluster_scripts
cluster_scripts
 
 
editing_tools
editing_tools
 
 
eglinking
eglinking
 
 
encode_submission
encode_submission
 
 
epimapAUX
epimapAUX
 
 
epimap_vis
epimap_vis
 
 
great_enrichment
great_enrichment
 
 
gwas_enrichment
gwas_enrichment
 
 
ic_eval
ic_eval
 
 
imputation_analysis
imputation_analysis
 
 
impute_vis
impute_vis
 
 
ldsc_enrichment
ldsc_enrichment
 
 
linking_methods
linking_methods
 
 
meme_enrichment
meme_enrichment
 
 
metadata_scripts
metadata_scripts
 
 
motif_enrichment
motif_enrichment
 
 
motifassoc_analysis
motifassoc_analysis
 
 
old_preprocessing_scripts
old_preprocessing_scripts
 
 
postprocessing_scripts
postprocessing_scripts
 
 
preprocessing_pipeline
preprocessing_pipeline
 
 
screen_comparison
screen_comparison
 
 
setup_scripts
setup_scripts
 
 
tree_vis
tree_vis
 
 
utils
utils
 
 
.gitignore
.gitignore
 
 
.tmp
.tmp
 
 
README.md
README.md
 
 
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
 
 
auxiliary_parsimony_functions.R
auxiliary_parsimony_functions.R
 
 
config_ChromImpute.sh
config_ChromImpute.sh
 
 
general_EPIMAP_ANALYSIS.R
general_EPIMAP_ANALYSIS.R
 
 
load_distance_matrices.R
load_distance_matrices.R
 
 
load_gwastree_analysis.R
load_gwastree_analysis.R
 
 
load_linking_data.py
load_linking_data.py
 
 
load_linking_objects.R
load_linking_objects.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_updated_validation_enrichments.R
load_updated_validation_enrichments.R
 
 
load_validation_gwastree_enrichments.R
load_validation_gwastree_enrichments.R
 
 
main_EPIMAP_ANALYSIS.R
main_EPIMAP_ANALYSIS.R
 
 

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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

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Epimap processing and analysis code repository

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