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Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis

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LDSC_Corces_etal_LDSC

LDSC_Corces_etal_LDSC

 
 

allelic_imbalance

allelic_imbalance

 
 

alzheimers-parkinsons-colocalization @ 29e228c

alzheimers-parkinsons-colocalization @ 29e228c

 
 

aux

aux

 
 

bam_merge

bam_merge

 
 

bulk_atacseq_preprocessing

bulk_atacseq_preprocessing

 
 

cluster_enrichment_for_gwas_hits

cluster_enrichment_for_gwas_hits

 
 

differential_accessibility_analysis

differential_accessibility_analysis

 
 

ld_expand_snps_final

ld_expand_snps_final

 
 

nn_interpretation

nn_interpretation

 
 

nn_training

nn_training

 
 

pca

pca

 
 

rev_resp/3i

rev_resp/3i

 
 

scoring_new_snps

scoring_new_snps

 
 

single_cell_atacseq_preprocessing

single_cell_atacseq_preprocessing

 
 

snp_interpretation

snp_interpretation

 
 

svm_pipeline

svm_pipeline

 
 

svm_snp_scoring

svm_snp_scoring

 
 

svm_training

svm_training

 
 

wasp_mapping_scripts

wasp_mapping_scripts

 
 

.gitignore

.gitignore

 
 

.gitmodules

.gitmodules

 
 

README.md

README.md

 
 

batches.filtered.csv

batches.filtered.csv

 
 

Repository files navigation

Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease

https://www.biorxiv.org/content/10.1101/2020.01.06.896159v1

Bulk ATAC-seq data processing / peak calling

scripts

Differential accessibility analysis with DESeq2 and limma voom

scripts

Single-cell ATAC-seq data processing / peak calling

scripts

LD score regression: Cell type specific analyses

scripts

Colocalization analysis

scripts

SVM model training

scripts

SNP effect scoring with SVMs

scripts

SNP effect interpretation

notebooks

Neural network training

scripts

Neural network interpretation/ variant score visualization

scripts

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Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis

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