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abc-enhancer-gene-prediction

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

atac-seq-pipeline

ENCODE ATAC-seq pipeline

awesome-cell-cell-communication

Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

azimuth_mapping_celltype_annotation.r

bed_statistics

A tool to compute various coverage statistics given a .bed file (i.e. a CLIP or ChIP-Seq result) and a reference genome.

brain-cell-type-peak-files

H3K27ac ChIPseq, H3K4me3 ChIPseq, ATACseq peak files for neurons, microglia, oligodendrocytes and astrocytes

brain_eye_comorbidity

ccgwas

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellect

CELLECT (CELL-type Expression-specific integration for Complex Traits)

cellex

CELLEX (CELL-type EXpression-specificity)

cellphonedb

cfea-pipeline

source code for our CFEA pipeline

children_myopia_incidence

chromegcn

Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

cibersortx

Repository for Cibersortx

clam

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

co_expression_pattern.r

coa

Integrative genomics analysis

coloc

Repo for the R package coloc

colocalization_for_two_traits

Code used for GWAS summary statistics

comparative_analysis.py

Script used for comparing the results from Sherlock analysis and MAGMA analysis at 3 different thresholds of P values

covid19_scrna

covid_balf

R script for the covid balf data analysis

ctdrtf

a computational method for identifying cell type-specific transcription factor relevant to complex diseases

ctdrtf_training

cytotalk

A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better characterization of cell-cell communication.

deepwas

DeepWAS: Directly integrating regulatory information into GWAS using machine learning

dleps

A Deep Learning based Efficacy Prediction System for drug discovery