fluff: exploratory analysis and visualization of high-throughput sequencing data

Non-canonical PRC1.1 Targets Active Genes Independent of H3K27me3 and Is Essential for Leukemogenesis

(2016) Vincent van den Boom et al.   Cell Reports

Is this the right normalization? A diagnostic tool for ChIP-seq normalization

(2015) Claudia Angelini et al.   BMC BIOINFORMATICS

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation

(2015) E. N. Kouwenhoven et al.   EMBO REPORTS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Embryonic transcription is controlled by maternally defined chromatin state

(2015) Saartje Hontelez et al.   Nature Communications

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) A. Akalin et al.   BIOINFORMATICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA

(2014) Ryan K. Dale et al.   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Binding of MBD2 Reveals Strong Preference for Highly Methylated Loci

(2014) Roberta Menafra et al.   PLoS One

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

(2014) S. Saeed et al.   SCIENCE

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

Heat maps

(2012) Nils Gehlenborg et al.   NATURE METHODS

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

An integrated ChIP-seq analysis platform with customizable workflows

(2011) Eugenia G Giannopoulou et al.   BMC BIOINFORMATICS

Data exploration

(2011) Noam Shoresh et al.   NATURE METHODS

Repitools: an R package for the analysis of enrichment-based epigenomic data

(2010) A. L. Statham et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY