Resources

Browsers

ONTIME Metabolomics Browser
ONTIME Metabolomics Browser – a browser that produces volcano plots and reading distributions from data from https://www.medrxiv.org/content/10.1101/2021.11.04.21265941v2 . Data was generated from KNIGHT-ADRC and DIAN cohorts.
Single-nuclei Brain RNA-seq expression browser
Single-nuclei Brain RNA-seq expression browser – a browser that displays expression of genes in brain cell types and displays fold change in expression in different cell types. Data is from https://www.medrxiv.org/content/10.1101/2021.11.04.21265941v2 and includes both sporadic and Mendelian cases of AD.
Single Nucleus Alzheimer disease RNA-seq Explorer (SNARE)
Single Nucleus Alzheimer disease RNA-seq Explorer (SNARE) – a visual exploration of data found in https://www.medrxiv.org/content/10.1101/2021.11.30.21267072v1?rss=1. Displays different cell types, disease status, TREM2, and sub-cluster.

Our Software/code

Omicser on Github
Omicser on Github – The NDCN Omics Browser that produces high quality browsers using shiny. The github contains the code and packages along with tutorials and examples.
NGI Docker repository
Docker repository – Container images from the NGI. Currently empty.
Harari Lab Github repositories
Harari Lab Github repositories – Scripts, pipelines, and browsers for data analysis. Includes RNAseq pipeline, metabolomics scripts, and transcriptomics browser.

Data Repositories

Knight ADRC Collection
Knight ADRC collection on NIAGADS – a collection of datasets generated from the Knight ADRC cohort. Includes GWAS, snRNAseq, whole exome sequencing, and summary statistics.
The Human Metabolome Database
The Human Metabolome Database – a database of human metabolites with pathways, several different types of search, and metabolomics studies.
ADNI – Alzheimer’s Disease Neuroimaging Initiative
ADNI – Alzheimer’s Disease Neuroimaging Initiative – A collection of MRI and PET scan images with associated genetic, clinical, and biomarker data. Features 4 cohorts, ADNI1, ADNI2, ADNIGO, and ADNI3.