Cargando…

MAnorm2 for quantitatively comparing groups of ChIP-seq samples

Eukaryotic gene transcription is regulated by a large cohort of chromatin-associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2, a new computational tool for quantitatively c...

Descripción completa

Detalles Bibliográficos
Autores principales:	Tu, Shiqi, Li, Mushan, Chen, Haojie, Tan, Fengxiang, Xu, Jian, Waxman, David J., Zhang, Yijing, Shao, Zhen
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory Press 2021
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7849384/ https://www.ncbi.nlm.nih.gov/pubmed/33208455 http://dx.doi.org/10.1101/gr.262675.120

Ejemplares similares

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

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

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

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

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

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

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

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

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

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
por: Bonhoure, Nicolas, et al.
Publicado: (2014)

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)

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

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

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)

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

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

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)

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

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data
por: Lundberg, Scott M., et al.
Publicado: (2016)

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)

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

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

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

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

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

SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin
por: Blanco, Enrique, et al.
Publicado: (2021)

Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
por: Morin, Alexander, et al.
Publicado: (2023)

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

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

Standardizing chromatin research: a simple and universal method for ChIP-seq
por: Arrigoni, Laura, et al.
Publicado: (2016)

Computational identification of cell-specific variable regions in ChIP-seq data
por: Andreani, Tommaso, et al.
Publicado: (2020)

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

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation
por: Aldridge, Sarah, et al.
Publicado: (2013)

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data
por: Teng, Mingxiang, et al.
Publicado: (2017)

MACE: model based analysis of ChIP-exo
por: Wang, Liguo, et al.
Publicado: (2014)

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

Cannot write session to /tmp/vufind_sessions/sess_7vekhtue4pni09p5fv9p5vib63