Downloadable Tools

  • AutoGenome, being developed by Wei Wang's group, is a pipeline to assist processing, visualization and analysis of sequencing data. It also provides access to the softwares such as ChromaSig and Chromia.
  • ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark.
  • ChromImpute is software for large-scale systematic epigenome imputation. ChromImpute takes an existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.
  • Epigram: A program to identify cis-elements that are predictive of epigenomic modifications.
  • RMAPBS: a short-read mapping tool specialized for mapping reads in bisulfite sequencing experiments included in the RMAP package. As with the original RMAP tool, RAMPBS can map reads with or without error probability information (quality scores). The RMAPBS algorithm was developed in a collaboration between the groups of Andrew Smith at USC and Michael Zhang at CSHL. For additional details see Smith et al. (2009).
  • TensorPute is software that can impute missing epigenetic assays. It uses tensor to represent high-dimensional epigenomic data of various assays in multiple cell types.

Hosted Tools

  • The Genboree Epigenome Toolset provides a web-based environment for scientists at all levels bioinformatics experience in which to conduct epigenomic analysis.
  • The STAR genome browser aims to provide an online browsing system that allows easy search and visualization of a large number of epigenomic data (the database contains 5,785 data sets in March 2012). Some new updates from the previous versions include 2D map of HiC data, in-browser analysis tools and save of the current configuration.