Cargando…

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of transcription factors and other DNA binding proteins. Computational ChIP-seq peak calling infers the location of protein–DNA interactions based on variou...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hansen, Peter, Hecht, Jochen, Ibrahim, Daniel M., Krannich, Alexander, Truss, Matthias, Robinson, Peter N.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory Press 2015
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561497/ https://www.ncbi.nlm.nih.gov/pubmed/26163319 http://dx.doi.org/10.1101/gr.189894.115

Ejemplares similares

Differential ATAC-seq and ChIP-seq peak detection using ROTS
por: Faux, Thomas, 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)

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

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

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

De novo ChIP-seq analysis
por: He, Xin, et al.
Publicado: (2015)

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
por: Hansen, Peter, et al.
Publicado: (2016)

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples
por: Chen, Haojie, et al.
Publicado: (2022)

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

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

Model-based Analysis of ChIP-Seq (MACS)
por: Zhang, Yong, et al.
Publicado: (2008)

Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
por: Gomes, Antonio L.C., et al.
Publicado: (2014)

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
por: Savic, Daniel, et al.
Publicado: (2015)

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq
por: Guertin, Michael J, et al.
Publicado: (2018)

Impact of sequencing depth in ChIP-seq experiments
por: Jung, Youngsook L., et al.
Publicado: (2014)

Inferring direct DNA binding from ChIP-seq
por: Bailey, Timothy L., et al.
Publicado: (2012)

AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification
por: Hiranuma, Naozumi, et al.
Publicado: (2019)

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

MAnorm2 for quantitatively comparing groups of ChIP-seq samples
por: Tu, Shiqi, et al.
Publicado: (2021)

seqMINER: an integrated ChIP-seq data interpretation platform
por: Ye, Tao, et al.
Publicado: (2011)

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information
por: Ma, Xiaotu, et al.
Publicado: (2012)

Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome
por: Karimzadeh, Mehran, et al.
Publicado: (2022)

Extracting transcription factor targets from ChIP-Seq data
por: Tuteja, Geetu, et al.
Publicado: (2009)

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
por: Blahnik, Kimberly R., et al.
Publicado: (2010)

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
por: Rye, Morten Beck, et al.
Publicado: (2011)

EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation
por: Lhoumaud, Priscillia, et al.
Publicado: (2019)

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
por: Liu, Peng, et al.
Publicado: (2016)

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

jMOSAiCS: joint analysis of multiple ChIP-seq datasets
por: Zeng, Xin, et al.
Publicado: (2013)

Optimized detection of transcription factor-binding sites in ChIP-seq experiments
por: Elo, Laura L., et al.
Publicado: (2012)

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)

ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles
por: Chen, Xi, et al.
Publicado: (2016)

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
por: Xu, Jinrui, et al.
Publicado: (2020)

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
por: Shao, Zhen, et al.
Publicado: (2012)

Optimized ChIP-seq method facilitates transcription factor profiling in human tumors
por: Singh, Abhishek A, et al.
Publicado: (2018)

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs
por: Berger, Severin, et al.
Publicado: (2019)

Inferring transcription factor complexes from ChIP-seq data
por: Whitington, Tom, et al.
Publicado: (2011)

Analysis of the epigenetic status of telomeres by using ChIP-seq data
por: Vaquero-Sedas, María I., et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_ueun1lu62aemm7bf578n8s3140