论文信息 - DiBind : Dierential binding analysis of ChIP-Seq peak data

DiBind : Dierential binding analysis of ChIP-Seq peak data

3 Example: Obtaining differentially bound sites 3 3.1 Reading in the peaksets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3.2 Counting reads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3.3 Establishing a contrast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3.4 Performing the differential analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3.5 Retrieving the differentially bound sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Rory Stark | Gord Brown | R. Stark | Gord Brown | Gordon D Brown

[1] Mark D. Robinson,et al. Moderated statistical tests for assessing differences in tag abundance , 2007, Bioinform..

[2] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[3] W. Huber,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[4] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[5] Peter J. Bickel,et al. Measuring reproducibility of high-throughput experiments , 2011, 1110.4705.

[6] Davis J. McCarthy,et al. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[7] Rory Stark. Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer , 2012, RECOMB.

[8] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.