Analysis and visualization of RNA-Seq expression data using rstudio, bioconductor, and integrated genome browser

Plant Functional Genomics: Methods and Protocols: Second Edition

Volumn , Issue , 2015, Pages 481-501

  Loraine, Ann E ^a   Blakley, Ivory Clabaugh ^a   Jagadeesan, Sridharan ^b   Harper, Jeff ^c   Miller, Gad ^d   Firon, Nurit ^b  

^a University of North Carolina at Charlotte   (United States)

^b VOLCANI CENTER   (Israel)

^c UNIVERSITY OF NEVADA   (United States)

^d BAR ILAN UNIVERSITY   (Israel)

Author keywords

Differential gene expression; edgeR; Integrated genome browser; Pollen; R; RNA Seq; Tomato; Visualization

Indexed keywords

RNA;

BIOLOGY; COMPUTER PROGRAM; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; TOMATO; WEB BROWSER;

COMPUTATIONAL BIOLOGY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LYCOPERSICON ESCULENTUM; RNA; SOFTWARE; WEB BROWSER;

EID: 84954578418     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4939-2444-8_24     Document Type: Chapter

References (9)

1. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536, PMID: 18423832
2. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-628, PMID: 18516045
3. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349, PMID: 18451266
4. Shendure J (2008) The beginning of the end for microarrays? Nat Methods 5:585-587, PMID:18587314
5. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140, PMID:19910308
6. Nikolayeva O, Robinson MD (2014) edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol 1150:45-79, PMID: 24743990
7. Oshlack A, Wakefield MJ (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 4:14, PMID: 19371405
8. Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25:2730-2731
9. Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq:accounting for selection bias. Genome Biol 11:R14 PMID: 20132535