Al-Esther

SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

Coronary_snATAC

limix_qtl

epuRate

A clean R Markdown template for your reports

onek1k_phase1

Contains code to analyze the OneK1K data and perform eQTL mapping of 14 cell types

ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

PFgenetics

Collaborative genetic studies of idiopathic pulmonary fibrosis

liger

R package for integrating and analyzing multiple single-cell datasets

GSSG

Gene Set + S2G strategy annotations analyzed for disease architecture

scScalpChromatin

ENCODE_CRISPR_data

Re-analyze and harmonize Gasperini et al., 2019, Schraivogel et al., 2020 and Nasser et al., 2021 data for ENCODE distal regulation E-G benchmarking

cisTopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

scRNA-seq_topic_modeling

Single Cell RNA-seq Analysis by Topic Modeling

Dev_Brain_IsoSeq

Bulk (CP/GZ) and single-cell Iso-Seq in the developing human brain

scRNA.seq.course

Analysis of single cell RNA-seq data course

LDSC

single-cell-benchmark

LDSCforRyten

S-LDSC scripts for use on MR server.

tabula-muris-senis

Tabula Muris Senis

jjAnno

An annotation package for ggplot plot

scGWAS

A method which leverages scRNA-seq data to achieve two goals: (1) to infer the cell types in which the disease-associated genes manifest and (2) to construct cellular modules which imply disease-specific activation of different processes.

AgingMouseBrainCCInx

Predicted cell-cell interactions of the aging mouse brain

scGWAS

scRNA_disease

Code for our paper: https://www.biorxiv.org/content/10.1101/528463v1

mouse-cerebellum-atac

CCI

Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information

banovichlab

Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).

developing-human-brain

adult-human-brain

Cytograph version used for adult human-brain analysis

PIMseq

repository for the package PIMseq