Using combined evidence from replicates to evaluate ChIP-seq peaks

JAMM: a peak finder for joint analysis of NGS replicates

(2014) Mahmoud M. Ibrahim et al.   BIOINFORMATICS

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

jMOSAiCS: joint analysis of multiple ChIP-seq datasets

(2013) Xin Zeng et al.   GENOME BIOLOGY

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY