regionReport: Interactive reports for region-level and feature-level genomic analyses

F1000Research

Volumn 4, Issue , 2016, Pages

  Collado Torres, Leonardo ^a,b,c   Jaffe, Andrew E ^a,b,c   Leek, Jeffrey T ^a,b,c  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c Johns Hopkins University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; PIPELINE; QUALITY CONTROL; REPRODUCIBILITY;

EID: 85010903572     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/F1000RESEARCH.6379.2     Document Type: Article

References (16)

1. Stark R, Brown G: DiffBind: differential binding analysis of ChIP-Seq peak data. 2011.
2. Jaffe AE, Murakami P, Lee H, et al.: Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol. 2012; 41(1): 200-209.
3. Torres LC, Frazee AC, Love MI, et al.: derfinder: Software for annotationagnostic RNA-seq differential expression analysis. bioRxiv. 2015; 015370.
4. Frazee AC, Sabunciyan S, Hansen KD, et al.: Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics. 2014; 15(3): 413-26.
5. Lawrence M, Huber W, Pagès H, et al.: Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9(8): e1003118.
6. Rosenbloom KR, Armstrong J, Barber GP, et al.: The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015; 43(Database issue): D670-D681.
7. Huber W, Carey VJ, Gentleman R, et al.: Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12(2): 115-121.
8. Love MI, Huber W, Anders S: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12): 550.
9. Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26(1): 139-140.
10. McCarthy DJ, Chen Y, Smyth GK: Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012; 40(10): 4288-4297.
11. Zhou X, Lindsay H, Robinson MD: Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res. 2014; 42(11): e91.
12. Sandve GK, Nekrutenko A, Taylor J, et al.: Ten simple rules for reproducible computational research. PLoS Comput Biol. 2013; 9(10): e1003285.
13. Xie Y: Dynamic Documents with R and knitr. CRC Press, 2013; 216.
14. Rstudio: RMarkdown: Dynamic Documents for R. 2014.
15. Hester J: Knitr Bootstrap framework, R package. 2015.
16. Collado-Torres L, Jaffe AE, Leek JT: derfinderPlot: Plotting functions for derfinder. 2015.