Methods for summarizing and visualizing multi-biosample functional genomic annotations

Toolkit for single-cell DNA methylation analysis.

Python package to analyze DNA methylation data

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

Bead-based single-cell atac processing

Predicting regulatory DNA elements based on epigenomic signatures

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python

Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape

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

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

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

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

U-Net for genomics

snakemake workflow for random forest based feature selection on chromHMM data

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

A Python library and command-line tool for creating dot-plots for pathways and enrichment analysis.

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