Cargando…

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE) Project. To this end, chromatin immunoprecipi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bailey, Timothy, Krajewski, Pawel, Ladunga, Istvan, Lefebvre, Celine, Li, Qunhua, Liu, Tao, Madrigal, Pedro, Taslim, Cenny, Zhang, Jie
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2013
Materias:	Education
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828144/ https://www.ncbi.nlm.nih.gov/pubmed/24244136 http://dx.doi.org/10.1371/journal.pcbi.1003326

Ejemplares similares

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

Analyzing ChIP-chip Data Using Bioconductor
por: Toedling, Joern, et al.
Publicado: (2008)

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

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

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
por: Landt, Stephen G., et al.
Publicado: (2012)

ChIPulate: A comprehensive ChIP-seq simulation pipeline
por: Datta, Vishaka, et al.
Publicado: (2019)

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)

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

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)

Systematic evaluation of factors influencing ChIP-seq fidelity
por: Chen, Yiwen, et al.
Publicado: (2012)

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
por: Xu, Jinrui, 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)

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

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

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

Normalization of ChIP-seq data with control
por: Liang, Kun, et al.
Publicado: (2012)

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

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

ChIPseqR: analysis of ChIP-seq experiments
por: Humburg, Peter, et al.
Publicado: (2011)

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)

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

DREME: motif discovery in transcription factor ChIP-seq data
por: Bailey, Timothy L.
Publicado: (2011)

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

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
por: Muhammad, Isiaka Ibrahim, et al.
Publicado: (2019)

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data
por: Wu, Song, et al.
Publicado: (2010)

SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs
por: Anand, Shankara, et al.
Publicado: (2019)

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking
por: Wu, George, et al.
Publicado: (2013)

Differential motif enrichment analysis of paired ChIP-seq experiments
por: Lesluyes, Tom, et al.
Publicado: (2014)

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

Successful implementation of ChIP-seq antibody quality control at Diagenode using automated ChIP protocol on the SX-8G IP-Star(®) Compact
por: Mazon, Ignacio, et al.
Publicado: (2013)

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

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

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

Widespread Misinterpretable ChIP-seq Bias in Yeast
por: Park, Daechan, et al.
Publicado: (2013)

In Silico Pooling of ChIP-seq Control Experiments
por: Sun, Guannan, 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)

Cannot write session to /tmp/vufind_sessions/sess_dhfi6ptcoll4tfofh31i3gn7uj