Cargando…

In Silico Pooling of ChIP-seq Control Experiments

As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation. Studying such variation requires individual level ChIP-seq experiments. Standard de...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sun, Guannan, Srinivasan, Rajini, Lopez-Anido, Camila, Hung, Holly A., Svaren, John, Keleş, Sündüz
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2014
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224375/ https://www.ncbi.nlm.nih.gov/pubmed/25380244 http://dx.doi.org/10.1371/journal.pone.0109691

Ejemplares similares

Normalization of ChIP-seq data with control
por: Liang, Kun, 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)

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

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

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments
por: Welch, Rene, et al.
Publicado: (2017)

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

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

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
por: Zhang, Qi, et al.
Publicado: (2016)

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
por: Chung, Dongjun, et al.
Publicado: (2013)

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)

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

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
por: Chung, Dongjun, et al.
Publicado: (2011)

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)

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

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)

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)

Modeling ChIP Sequencing In Silico with Applications
por: Zhang, Zhengdong D., et al.
Publicado: (2008)

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)

Design and analysis of ChIP-seq experiments for DNA-binding proteins
por: Kharchenko, Peter V., et al.
Publicado: (2008)

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

Leveraging biological replicates to improve analysis in ChIP-seq experiments
por: Yang, Yajie, et al.
Publicado: (2014)

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

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)

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

jChIP: a graphical environment for exploratory ChIP-Seq data analysis
por: Chojnowski, Krzysztof, et al.
Publicado: (2014)

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
por: Oki, Shinya, et al.
Publicado: (2018)

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

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

Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data
por: Ghosh, Debashis, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_i6vqecfqf7bov34mso4br8mnu4