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asoc

Code for part of the computational analysis in the paper 'Allele-specific open chromatin in human iPSC neurons elucidates functional noncoding disease variants'

asoc_qtl_enrichment

Enrichment analyses of allele-specific chromatin accessibility variants

atacseq_pipeline

A Snakemake pipeline for processing ATAC-seq reads from various samples into a peak count matrix

better-qqplots

python code for creating high quality qq-plots

bvs_cre-gene

A Bayesian variable selection method that models the relationship between the activity of cis-regulatory elements and target gene expression

crop-seq

Differential expression analysis on single-cell CROP-seq data (neural progenitor cells)

crop-seq2

Differential expression analysis on single-cell CROP-seq data (Glutamatergic neurons)

gene_regulation

website of preliminary analyses

gsfa_in_house

In-house scripts for the GSFA project

gsfa_site

Guided Sparse Factor Analysis (GSFA) on perturbed single-cell RNA-seq data: https://gradonion.github.io/GSFA_site/

scalefaster

R package for efficient centering and scaling of matrix

website