gradonion

ASoC_functional_disease_variants

Allele-specific open chromatin in human iPSC neurons elucidates functional noncoding disease variants

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)

GSFA_site

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

GSFA

R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single-cell CRISPR screening data.

GSFA_paper

Analysis code for the GSFA manuscript "A novel Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening"

gradonion/ATACseq_pipeline

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

gradonion/ASoC

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

gradonion/BVS_cre-gene

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

gradonion/CROP-seq

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

gradonion/GSFA_site

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

gradonion/ASoC_QTL_enrichment

Enrichment analyses of allele-specific chromatin accessibility variants

gradonion/better-qqplots

python code for creating high quality qq-plots

gradonion/CROP-seq2

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

gradonion/gene_regulation

website of preliminary analyses

gradonion/GSFA_in_house

In-house scripts for the GSFA project

gradonion/scalefaster

R package for efficient centering and scaling of matrix

gradonion/website