Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Genomic location analysis by ChIP-Seq

(2009) Artem Barski et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

(2008) A. P. Fejes et al.   BIOINFORMATICS

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

(2008) David A Nix et al.   BMC BIOINFORMATICS

Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq

(2008) Yong Zhang et al.   BMC GENOMICS

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY