Cargando…

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes

Graph-based representations are considered to be the future for reference genomes, as they allow integrated representation of the steadily increasing data on individual variation. Currently available tools allow de novo assembly of graph-based reference genomes, alignment of new read sets to the gra...

Descripción completa

Detalles Bibliográficos
Autores principales:	Grytten, Ivar, Rand, Knut D., Nederbragt, Alexander J., Storvik, Geir O., Glad, Ingrid K., Sandve, Geir K.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2019
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396939/ https://www.ncbi.nlm.nih.gov/pubmed/30779737 http://dx.doi.org/10.1371/journal.pcbi.1006731

Ejemplares similares

Coordinates and intervals in graph-based reference genomes
por: Rand, Knut D., et al.
Publicado: (2017)

Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods
por: Grytten, Ivar, et al.
Publicado: (2020)

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

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels
por: Grytten, Ivar, et al.
Publicado: (2022)

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

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

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

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

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)

HiChIP-Peaks: a HiChIP peak calling algorithm
por: Shi, Chenfu, et al.
Publicado: (2020)

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

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)

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
por: Müller, Lydia, et al.
Publicado: (2016)

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)

Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes
por: Sharma, Vasudha, et al.
Publicado: (2020)

Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression
por: Handel, Adam E, et al.
Publicado: (2013)

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)

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

peaksat: an R package for ChIP-seq peak saturation analysis
por: Boyd, Joseph R, et al.
Publicado: (2023)

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

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data
por: Nakato, Ryuichiro, et al.
Publicado: (2013)

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)

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

A varying threshold method for ChIP peak-calling using multiple sources of information
por: Chen, Kuan-Bei, et al.
Publicado: (2010)

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

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information
por: Wu, Hao, et al.
Publicado: (2014)

Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information
por: Osmanbeyoglu, Hatice Ulku, et al.
Publicado: (2012)

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)

Unsupervised Contrastive Peak Caller for ATAC-seq
por: Vu, Ha T.H., et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_alkt8popt7eec63s480bhptc9m