snATAC_MDD

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## [Single-nucleus chromatin accessibility profiling identifies cell types and functional variants contributing to major depression](https://www.biorxiv.org/content/10.1101/2023.10.02.560567v1)

Anjali Chawla, Doruk Cakmakci, Laura M. Fiori, Wenmin Zhang, Malosree Maitra, Jennie Yang, Dariusz Żurawek, Gabriella Frosi, Reza Rahimian, Haruka Mitsuhashi, MA Davoli, Ryan Denniston, Gary Gang Chen, Volodymyr Yerko, Deborah Mash, Kiran Girdhar, Schahram Akbarian, Naguib Mechawar, Matthew Suderman, Yue Li\*, Corina Nagy\*, Gustavo Turecki*#
 \*Shared senior authorship, #Corresponding authorship, [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.10.02.560567v1)

## Preprocessing snATAC-seq data, demultiplexing male and female nuclei, matching with external genotypes

[scripts](https://github.com/MGSSdouglas/snATAC_MDD/blob/main/1_preprocessing/README.md)

## Generating snATAC-seq project, dimensionality-reduction, clustering, annotating cell types and clusters

[scripts](https://github.com/MGSSdouglas/snATAC_MDD/blob/main/2_clustering/README.md)

## Differential cCREs and TF motifs in MDD versus control subjects, cell types and clusters-specific markers, cluster-specific TF gene regulatory networks

[scripts](https://github.com/MGSSdouglas/snATAC_MDD/blob/main/3_differential_analysis/README.md)

## Cluster-specific heritability enrichment of MDD GWAS SNPs (S-LDSC, HESS, fine-mapping)

[scripts](https://github.com/MGSSdouglas/snATAC_MDD/blob/main/4_heritability_enrichment/README.md)

## Cluster-specific gapped kmer SVMs (ISM, deltaSVM, gkmExplain) to identify MDD risk variants

[scripts](https://github.com/MGSSdouglas/snATAC_MDD/blob/main/5_gapped_kmer_svm/README.md)

## Multi-modal visualization of MDD SNPs (DLPFC 3D chromatin loops and histone modifications)

[scripts](https://github.com/MGSSdouglas/snATAC_MDD/blob/main/6_snp_visualization/README.md)

## Allelic Imbalance Analysis (snATAC and snRNA)

[scripts](https://github.com/MGSSdouglas/snATAC_MDD/blob/main/7_allelic_imbalance/README.md)

snATAC_MDD

snATAC_MDD Latest Version Download

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