GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Authors
Keywords
Bioconductor Package, Chromatin Interaction, Interaction Landscape, Enhancer Interaction, Individual Anchor
Journal
BMC GENOMICS
Volume 16, Issue 1, Pages -
Publisher
Springer Nature
Online
2015-11-17
DOI
10.1186/s12864-015-2140-x
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Mango: a bias-correcting ChIA-PET analysis pipeline
- (2015) Douglas H. Phanstiel et al. BIOINFORMATICS
- FourCSeq: analysis of 4C sequencing data
- (2015) Felix A. Klein et al. BIOINFORMATICS
- diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
- (2015) Aaron T.L. Lun et al. BMC BIOINFORMATICS
- Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
- (2014) Carolin Walter et al. BIOINFORMATICS
- Genome-wide map of regulatory interactions in the human genome
- (2014) Nastaran Heidari et al. GENOME RESEARCH
- Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
- (2014) F. Ay et al. GENOME RESEARCH
- PIM Kinases Are Essential for Chronic Lymphocytic Leukemia Cell Survival (PIM2/3) and CXCR4-Mediated Microenvironmental Interactions (PIM1)
- (2014) S. Decker et al. MOLECULAR CANCER THERAPEUTICS
- A promoter-level mammalian expression atlas
- (2014) NATURE
- Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment
- (2014) Jim R Hughes et al. NATURE GENETICS
- Transcriptional enhancers: from properties to genome-wide predictions
- (2014) Daria Shlyueva et al. NATURE REVIEWS GENETICS
- A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
- (2014) Jonas Paulsen et al. NUCLEIC ACIDS RESEARCH
- visPIG - A Web Tool for Producing Multi-Region, Multi-Track, Multi-Scale Plots of Genetic Data
- (2014) Matthew Scales et al. PLoS One
- Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements
- (2014) Petros Kolovos et al. Epigenetics & Chromatin
- BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders
- (2013) F. Damm et al. BLOOD
- Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
- (2013) Jennifer E. Phillips-Cremins et al. CELL
- Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
- (2013) V. C. Seitan et al. GENOME RESEARCH
- The Hierarchy of the 3D Genome
- (2013) Johan H. Gibcus et al. MOLECULAR CELL
- Chromatin Insulators: Linking Genome Organization to Cellular Function
- (2013) Jennifer E. Phillips-Cremins et al. MOLECULAR CELL
- Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations
- (2013) Yubo Zhang et al. NATURE
- Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
- (2013) Job Dekker et al. NATURE REVIEWS GENETICS
- r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data
- (2013) Supat Thongjuea et al. NUCLEIC ACIDS RESEARCH
- The UCSC Genome Browser database: 2014 update
- (2013) Donna Karolchik et al. NUCLEIC ACIDS RESEARCH
- Chromatin and epigenetic features of long-range gene regulation
- (2013) N. Harmston et al. NUCLEIC ACIDS RESEARCH
- Software for Computing and Annotating Genomic Ranges
- (2013) Michael Lawrence et al. PLoS Computational Biology
- HiTC: exploration of high-throughput ‘C’ experiments
- (2012) Nicolas Servant et al. BIOINFORMATICS
- Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor
- (2012) Wulan Deng et al. CELL
- Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
- (2012) Guoliang Li et al. CELL
- Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
- (2012) Iouri Chepelev et al. CELL RESEARCH
- Hi–C: A comprehensive technique to capture the conformation of genomes
- (2012) Jon-Matthew Belton et al. METHODS
- The long-range interaction landscape of gene promoters
- (2012) Amartya Sanyal et al. NATURE
- A map of the cis-regulatory sequences in the mouse genome
- (2012) Yin Shen et al. NATURE
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate
- (2012) Yin C Lin et al. NATURE IMMUNOLOGY
- Iterative correction of Hi-C data reveals hallmarks of chromosome organization
- (2012) Maxim Imakaev et al. NATURE METHODS
- Integrative annotation of chromatin elements from ENCODE data
- (2012) Michael M. Hoffman et al. NUCLEIC ACIDS RESEARCH
- Role of nuclear receptor NR4A2 in gastrointestinal inflammation and cancers
- (2012) Yi-Fang Han WORLD JOURNAL OF GASTROENTEROLOGY
- Reduced NR4A gene dosage leads to mixed myelodysplastic/myeloproliferative neoplasms in mice
- (2011) A. M. Ramirez-Herrick et al. BLOOD
- Dynamic long-range chromatin interactions controlMybproto-oncogene transcription during erythroid development
- (2011) Ralph Stadhouders et al. EMBO JOURNAL
- The nuclear orphan receptor Nr4a2 induces Foxp3 and regulates differentiation of CD4+ T cells
- (2011) Takashi Sekiya et al. Nature Communications
- 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
- The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture
- (2010) Julien Dorier et al. NUCLEIC ACIDS RESEARCH
- ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
- (2010) Guoliang Li et al. GENOME BIOLOGY
- Nurr1 Is Required for Maintenance of Maturing and Adult Midbrain Dopamine Neurons
- (2009) B. Kadkhodaei et al. JOURNAL OF NEUROSCIENCE
- An oestrogen-receptor-α-bound human chromatin interactome
- (2009) Melissa J. Fullwood et al. NATURE
- Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
- (2009) Stefan Schoenfelder et al. NATURE GENETICS
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription
- (2008) Takanori Amano et al. DEVELOPMENTAL CELL
- Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
- (2008) Lars Guelen et al. NATURE
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started