ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates
Authors
Keywords
ChIP-seq, ATAC-seq, Reproducibility, Transcription factor, Transcriptional regulation
Journal
GENOMICS
Volume 113, Issue 4, Pages 1855-1866
Publisher
Elsevier BV
Online
2021-04-19
DOI
10.1016/j.ygeno.2021.04.026
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Expanded encyclopaedias of DNA elements in the human and mouse genomes
- (2020) Jill E. Moore et al. NATURE
- BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates
- (2018) Emily Goren et al. BIOINFORMATICS
- Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
- (2016) Lydia Müller et al. BMC BIOINFORMATICS
- Using combined evidence from replicates to evaluate ChIP-seq peaks
- (2015) Vahid Jalili et al. BIOINFORMATICS
- JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
- (2015) Anthony Mathelier et al. NUCLEIC ACIDS RESEARCH
- PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
- (2014) Yanxiao Zhang et al. BIOINFORMATICS
- LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS
- (2014) Yajie Yang et al. Computational and Structural Biotechnology Journal
- The exact probability distribution of the rank product statistics for replicated experiments
- (2013) Rob Eisinga et al. FEBS LETTERS
- Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
- (2013) Timothy Bailey et al. PLoS Computational Biology
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- (2012) S. G. Landt et al. GENOME RESEARCH
- Identifying ChIP-seq enrichment using MACS
- (2012) Jianxing Feng et al. Nature Protocols
- ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
- (2012) Terrence S. Furey NATURE REVIEWS GENETICS
- High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
- (2012) Yuchun Guo et al. PLoS Computational Biology
- Measuring reproducibility of high-throughput experiments
- (2011) Qunhua Li et al. Annals of Applied Statistics
- MEME-ChIP: motif analysis of large DNA datasets
- (2011) Philip Machanick et al. BIOINFORMATICS
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- Comments on the rank product method for analyzing replicated experiments
- (2010) James A. Koziol FEBS LETTERS
- A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
- (2010) Morten Beck Rye et al. NUCLEIC ACIDS RESEARCH
- Repeatability of published microarray gene expression analyses
- (2009) John P A Ioannidis et al. NATURE GENETICS
- MEME SUITE: tools for motif discovery and searching
- (2009) T. L. Bailey et al. NUCLEIC ACIDS RESEARCH
- Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
- (2008) David A Nix et al. BMC BIOINFORMATICS
- Design and analysis of ChIP-seq experiments for DNA-binding proteins
- (2008) Peter V Kharchenko et al. NATURE BIOTECHNOLOGY
- Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
- (2008) R. Jothi et al. NUCLEIC ACIDS RESEARCH
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started