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m-makarious merged 1 commit into from
Oct 24, 2025
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Update README.md #3

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14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -20,11 +20,11 @@ Our reference datasets consisted of summary statistics from previously published
* Latino GWAS meta-analysis; Loesch et al 2021; [see here](https://ndkp.hugeamp.org/dinspector.html?dataset=Loesch2021_Parkinsons_HS)

• Alzheimer's disease
- AD GWAS meta-analysis; Bellenguez et al 2022; https://www.ebi.ac.uk/gwas/ (accession no. GCST90027158)
* FinnGen Release 6; [see here](https://r6.finngen.fi/pheno/G6_AD_WIDE_EXMORE)
* African American GWAS meta-analysis; Kunkle 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33074286)
* East Asian GWAS meta-analysis; Shigemizu et al 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33654092)
* Latino GWAS meta-analysis; Lake et al 2023; [see here](https://ndkp.hugeamp.org/dinspector.html?dataset=Lake2023_AD_Mixed)
* AD GWAS meta-analysis; Bellenguez et al 2022; https://www.ebi.ac.uk/gwas/ (accession no. GCST90027158)
* European AD GWAS meta-analysis; [see here](https://dss.niagads.org/datasets/ng00075/)
* African American GWAS meta-analysis; Kunkle 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33074286)
* East Asian GWAS meta-analysis; Shigemizu et al 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33654092)
* Latino GWAS meta-analysis; Lake et al 2023; [see here](https://ndkp.hugeamp.org/dinspector.html?dataset=Lake2023_AD_Mixed)

### Helpful Links
- *coming soon* pre-print
Expand All @@ -44,7 +44,7 @@ Our reference datasets consisted of summary statistics from previously published
├── analyses
│   ├── 00_clean_and_prep_PD.ipynb
│   ├── 01_PAR_calculations_PD.ipynb
│   ├── 02_clean_and_prep_AD.ipynb
│   ├── 02_clean_and_prep_AD_revised.ipynb
│   ├── 03_PAR_calculations_AD.ipynb
│   ├── 04_PD_EUR_fine_mapping.ipynb
│   ├── 05_PD_AFR_fine_mapping.ipynb
Expand All @@ -69,7 +69,7 @@ Our reference datasets consisted of summary statistics from previously published
|:-----------------------------:|:------------------------------------------------------------------------------------------------------------------------------------------------:|
| 00_clean_and_prep_PD.ipynb | Load list of 90 PD risk loci from Nalls publication, import ancestry-specific GWAS summary statistics, select top hits, and identify known/population-specific variants for analysis. |
| 01_PAR_calculations_PD.ipynb | Calculate population attributable risk (PAR) for each target and generate a table with summary statistics and PAR. |
| 02_clean_and_prep_AD.ipynb | Import AD datasets for each ancestry, clean and filter p-values < 0.05, select top hits for each ancestry, and generate dataset for calculations. |
| 02_clean_and_prep_AD_revised.ipynb | Import AD datasets for each ancestry, clean and filter p-values < 0.05, select top hits for each ancestry, and generate dataset for calculations. |
| 03_PAR_calculations_AD.ipynb | Calculate population attributable risk (PAR) for each target and generate a table with summary statistics and PAR. |
| 04_PD_EUR_fine_mapping.ipynb | Extract chromosome and base pair positions from summary statistics for selected loci in EUR population, perform fine-mapping, and save results. |
| 05_PD_AFR_fine_mapping.ipynb | Extract chromosome and base pair positions from summary statistics for selected loci in AFR population, perform fine-mapping, and save results. |
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