Cargando…

peaksat: an R package for ChIP-seq peak saturation analysis

BACKGROUND: Epigenomic profiling assays such as ChIP-seq have been widely used to map the genome-wide enrichment profiles of chromatin-associated proteins and posttranslational histone modifications. Sequencing depth is a key parameter in experimental design and quality control. However, due to vari...

Descripción completa

Detalles Bibliográficos
Autores principales:	Boyd, Joseph R, Gao, Cong, Quinn, Kathleen, Fritz, Andrew, Stein, Janet, Stein, Gary, Glass, Karen, Frietze, Seth
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9878872/ https://www.ncbi.nlm.nih.gov/pubmed/36698077 http://dx.doi.org/10.1186/s12864-023-09109-7

Ejemplares similares

BayesPeak—an R package for analysing ChIP-seq data
por: Cairns, Jonathan, et al.
Publicado: (2011)

PeakRanger: A cloud-enabled peak caller for ChIP-seq data
por: Feng, Xin, et al.
Publicado: (2011)

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks
por: Hansen, Peter, et al.
Publicado: (2015)

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
por: Zhu, Lihua J, et al.
Publicado: (2010)

Shape-based peak identification for ChIP-Seq
por: Hower, Valerie, et al.
Publicado: (2011)

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
por: Wu, George, et al.
Publicado: (2013)

BayesPeak: Bayesian analysis of ChIP-seq data
por: Spyrou, Christiana, et al.
Publicado: (2009)

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
por: Wilbanks, Elizabeth G., et al.
Publicado: (2010)

COPAR: A ChIP-Seq Optimal Peak Analyzer
por: Tang, Binhua, et al.
Publicado: (2017)

Differential ATAC-seq and ChIP-seq peak detection using ROTS
por: Faux, Thomas, et al.
Publicado: (2021)

OccuPeak: ChIP-Seq Peak Calling Based on Internal Background Modelling
por: de Boer, Bouke A., et al.
Publicado: (2014)

Differential peak calling of ChIP-seq signals with replicates with THOR
por: Allhoff, Manuel, et al.
Publicado: (2016)

Features that define the best ChIP-seq peak calling algorithms
por: Thomas, Reuben, et al.
Publicado: (2017)

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data
por: Carroll, Thomas S., et al.
Publicado: (2014)

D-peaks: A visual tool to display ChIP-seq peaks along the genome
por: Brohée, Sylvain, et al.
Publicado: (2012)

Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
por: Kruczyk, Marcin, et al.
Publicado: (2013)

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
por: Grytten, Ivar, et al.
Publicado: (2019)

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
por: Micsinai, Mariann, et al.
Publicado: (2012)

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
por: Kornacker, Karl, et al.
Publicado: (2012)

RECAP reveals the true statistical significance of ChIP-seq peak calls
por: Chitpin, Justin G, et al.
Publicado: (2019)

WACS: improving ChIP-seq peak calling by optimally weighting controls
por: Awdeh, Aseel, et al.
Publicado: (2021)

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data
por: Chen, Yiwen, et al.
Publicado: (2011)

NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data
por: Kim, Nak-Kyeong, et al.
Publicado: (2013)

An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data
por: Ji, Hongkai, et al.
Publicado: (2008)

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
por: Ho, Joshua WK, et al.
Publicado: (2011)

ChIP-Enrich: gene set enrichment testing for ChIP-seq data
por: Welch, Ryan P., et al.
Publicado: (2014)

ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis
por: Suryatenggara, Jeremiah, et al.
Publicado: (2021)

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages
por: Park, Seung-Jin, et al.
Publicado: (2017)

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data
por: Cao, Yingying, et al.
Publicado: (2020)

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
por: Thomas-Chollier, Morgane, et al.
Publicado: (2012)

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
por: Nix, David A, et al.
Publicado: (2008)

Combining multiple ChIP-seq peak detection systems using combinatorial fusion
por: Schweikert, Christina, et al.
Publicado: (2012)

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains
por: Starmer, Joshua, et al.
Publicado: (2016)

Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks
por: Laczik, Miklós, et al.
Publicado: (2016)

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution
por: Mendoza-Parra, Marco-Antonio, et al.
Publicado: (2013)

The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments
por: Wiegreffe, Daniel, et al.
Publicado: (2018)

Comparative analysis of commonly used peak calling programs for ChIP-Seq analysis
por: Jeon, Hyeongrin, et al.
Publicado: (2020)

CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection
por: Oh, Dongpin, et al.
Publicado: (2020)

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data
por: Barozzi, Iros, et al.
Publicado: (2011)

Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
por: Buisine, Nicolas, et al.
Publicado: (2009)

Cannot write session to /tmp/vufind_sessions/sess_opvuiqhr48c94bt3vclasnbcr1