General Resources for Epigenomics
- Avocado - About Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.
- APEC - Single cell epigenomic clustering based on accessibility pattern
- cisTopic - cisTopic is an R-package to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
- Episcanpy - EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data.
- Peax - Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
- REPTILE - REPTILE is a tool to identify the precise location of enhancers by integrating histone modification data and base-resolution DNA methylation profiles.
- Haystack - Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
- pipelines - Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data
- TCGAWorkflow - Analyze cancer genomics and epigenomics data using Bioconductor packages