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project analyzing Y chromosome variants, genes and haplogroups in Parkinson's disease.

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Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
1_data_prep		1_data_prep
2_call_haplogroups		2_call_haplogroups
3_analyze_haplogroups		3_analyze_haplogroups
4_haplogroup_logistic_regression		4_haplogroup_logistic_regression
5_haplogroup_variant_annotation		5_haplogroup_variant_annotation
6_gene_expression		6_gene_expression
README.md		README.md

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Analysis of Y Chromosome Haplogroups in PD

Author(s) - Frank Grenn

Quick Description:

Project looking at Y chromosome variants, genes and haplogroups in PD. Uses data from AMP-PD, NeuroX, NABEC and UKBioBank.

1. Tools and Modules

Tools:

Biowulf Modules:

R
Python
Plink
Flashpca
ANNOVAR
metal

2. Code Overview

Each folder has a group of notebooks/scripts for a part of the project.
These should be run in their numbered order if you are redoing the analyses.