Cargando…

A short survey of computational analysis methods in analysing ChIP-seq data

Chromatin immunoprecipitation followed by massively parallel next-generation sequencing (ChIP-seq) is a valuable experimental strategy for assaying protein-DNA interaction over the whole genome. Many computational tools have been designed to find the peaks of the signals corresponding to protein bin...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kim, Hyunmin, Kim, Jihye, Selby, Heather, Gao, Dexiang, Tong, Tiejun, Lip Phang, Tzu, Choon Tan, Aik
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Software Review
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525234/ https://www.ncbi.nlm.nih.gov/pubmed/21296745 http://dx.doi.org/10.1186/1479-7364-5-2-117

Ejemplares similares

A survey of statistical software for analysing RNA-seq data
por: Gao, Dexiang, et al.
Publicado: (2010)

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

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
por: Ambrosini, Giovanna, et al.
Publicado: (2016)

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

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
por: Yan, Huihuang, et al.
Publicado: (2014)

An integrated ChIP-seq analysis platform with customizable workflows
por: Giannopoulou, Eugenia G, et al.
Publicado: (2011)

CHANCE: comprehensive software for quality control and validation of ChIP-seq data
por: Diaz, Aaron, et al.
Publicado: (2012)

CSA: a web service for the complete process of ChIP-Seq analysis
por: Li, Min, et al.
Publicado: (2019)

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
por: Khomtchouk, Bohdan B., et al.
Publicado: (2016)

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
por: Qin, Qian, et al.
Publicado: (2016)

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

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
por: Trinh, Quang M, et al.
Publicado: (2013)

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

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

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
por: Ather, Syed Hussain, et al.
Publicado: (2020)

A comprehensive comparison of tools for differential ChIP-seq analysis
por: Steinhauser, Sebastian, et al.
Publicado: (2016)

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

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data
por: Buck, Michael J, et al.
Publicado: (2005)

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

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
por: Toedling, Joern, et al.
Publicado: (2007)

A flexible ChIP-sequencing simulation toolkit
por: Zheng, An, et al.
Publicado: (2021)

ChIPseek, a web-based analysis tool for ChIP data
por: Chen, Ting-Wen, et al.
Publicado: (2014)

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
por: Muiño, Jose M, et al.
Publicado: (2011)

Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators
por: Piechota, Marcin, et al.
Publicado: (2016)

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis
por: Cormier, Nathan, et al.
Publicado: (2016)

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes
por: Polit, Lélia, et al.
Publicado: (2021)

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
por: Zacher, Benedikt, et al.
Publicado: (2010)

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

MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates
por: Bérard, Caroline, et al.
Publicado: (2013)

Software for rapid time dependent ChIP-sequencing analysis (TDCA)
por: Myschyshyn, Mike, et al.
Publicado: (2017)

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

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)

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)

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

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data
por: Lun, Aaron T. L., et al.
Publicado: (2016)

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data
por: Lan, Xun, et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_nmtah3q4o9vep511eev811vr4r