Methods for summarizing and visualizing multi-biosample functional genomic annotations

Python package to analyze DNA methylation data

Toolkit for single-cell DNA methylation analysis.

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

Bead-based single-cell atac processing

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

Predicting regulatory DNA elements based on epigenomic signatures

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

Genome-wide extraction of real-valued signals hidden in noisy multisample HTS data

EpiVerse is an innovative three-stage pipeline designed to impute chromatin structures across various cell types. By enabling cross cell-type Hi-C imputations, EpiVerse facilitates unique "epigenome-level" perturbational Hi-C experiments, offering valuable insights into chromatin architecture dynamics under diverse epigenetic conditions.

A standardised workflow to explore and analyse prokaryotic methylation patterns for Nanopore sequencing 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.

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

snakemake workflow for random forest based feature selection on chromHMM data