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.
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.