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Open Source Science

https://github.com/kundajelab/alzheimers_parkinsons

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

https://github.com/kundajelab/alzheimers_parkinsons

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 1 DOI reference(s) in README
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    Academic publication links
    Links to: biorxiv.org
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (3.0%) to scientific vocabulary
Last synced: 4 months ago · JSON representation

Repository

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

Basic Info
  • Host: GitHub
  • Owner: kundajelab
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 279 MB
Statistics
  • Stars: 44
  • Watchers: 11
  • Forks: 14
  • Open Issues: 1
  • Releases: 0
Created almost 7 years ago · Last pushed over 5 years ago

https://github.com/kundajelab/alzheimers_parkinsons/blob/master/ 

# Single-cell epigenomic identification of inherited risk loci in Alzheimers and Parkinsons disease
https://www.biorxiv.org/content/10.1101/2020.01.06.896159v1


## Bulk ATAC-seq data processing / peak calling ##
[scripts](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/bulk_atacseq_preprocessing)

## Differential accessibility analysis with DESeq2 and limma voom ##
[scripts](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/differential_accessibility_analysis)

## Single-cell ATAC-seq data processing / peak calling ##
[scripts](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/single_cell_atacseq_preprocessing)

## LD score regression: Cell type specific analyses ##
[scripts](https://github.com/lfresard/LDSC_Corces_etal_LDSC/tree/5bcf805562c72575cd2e614194c888af9a946407)

## Colocalization analysis ##
[scripts](https://github.com/mikegloudemans/alzheimers-parkinsons-colocalization/tree/29e228c1cdd68f1fd10ff84bea26b95e4faac7ba)

## SVM model training ##
[scripts](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/svm_training)

## SNP effect scoring with SVMs ##
[scripts](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/svm_snp_scoring)

## SNP effect interpretation ##
[notebooks](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/snp_interpretation)

## Neural network training ##
[scripts](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/nn_training)

## Neural network interpretation/ variant score visualization ##
[scripts](https://github.com/kundajelab/alzheimers_parkinsons/tree/master/nn_interpretation)

Owner

  • Name: Kundaje Lab
  • Login: kundajelab
  • Kind: organization
  • Location: Stanford University

Compbio and machine learning code repositories from the Kundaje Lab at Stanford Genetics and Computer Science Depts.

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