LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

ColoWeb: a resource for analysis of colocalization of genomic features

(2015) RyangGuk Kim et al.   BMC GENOMICS

Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression

(2015) Y. V. Kravatsky et al.   DNA RESEARCH

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

(2015) Eleni M. Tomazou et al.   Cell Reports

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

genomation: a toolkit to summarize, annotate and visualize genomic intervals

(2014) A. Akalin et al.   BIOINFORMATICS

Comprehensive analysis of DNA methylation data with RnBeads

(2014) Yassen Assenov et al.   NATURE METHODS

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

(2014) Manuel Sánchez-Castillo et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool

(2013) Raymond K. Auerbach et al.   BIOINFORMATICS

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

The Genomic HyperBrowser: an analysis web server for genome-scale data

(2013) Geir K. Sandve et al.   NUCLEIC ACIDS RESEARCH

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells

(2012) Christoph Bock et al.   MOLECULAR CELL

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data

(2009) Christoph Bock et al.   GENOME BIOLOGY