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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
 
 

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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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