Repo for code for using the MultiSNP-expecto tool and analysis pipeline

Training an interpretation of ensemble of convolutional neural networks for multi-task functional genomic classification tasks.

A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data

Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.

Methods for training and interpretation of an ensemble of neural networks for multi-task functional prediction of accessibility or histone modifications from DNA sequence.

Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape

Resource for summarizing and tracking new array samples published to NCBI's Gene Expression Omnibus (GEO) database.

Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)

chromatin accessibility predictions with attention mechanism

Latent representation of the human pan-celltype epigenome through a deep recurrent neural network.

The data preprocessing pipeline for the VISION project (for human data)

The data preprocessing pipeline for the Gtex project (for human data)

Find risk snp in the LD region of GWAS snps by convolutional neural network

Lab data processing pipelines

Home of the SCIDDO tool

U-Net for genomics

snakemake workflow for random forest based feature selection on chromHMM data

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)