| Chapter title |
Analysis and visualization of RNA-Seq expression data using RStudio, Bioconductor, and Integrated Genome Browser
|
|---|---|
| Chapter number | 24 |
| Book title |
Plant Functional Genomics
|
| Published in |
Methods in molecular biology, January 2015
|
| DOI | 10.1007/978-1-4939-2444-8_24 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-2443-1, 978-1-4939-2444-8
|
| Authors |
Ann E Loraine, Ivory Clabaugh Blakley, Sridharan Jagadeesan, Jeff Harper, Gad Miller, Nurit Firon, Ann E. Loraine, Loraine, Ann E., Blakley, Ivory Clabaugh, Jagadeesan, Sridharan, Harper, Jeff, Miller, Gad, Firon, Nurit |
| Abstract |
Sequencing costs are falling, but the cost of data analysis remains high, often because unforeseen problems arise, such as insufficient depth of sequencing or batch effects. Experimenting with data analysis methods during the planning phase of an experiment can reveal unanticipated problems and build valuable bioinformatics expertise in the organism or process being studied. This protocol describes using R Markdown and RStudio, user-friendly tools for statistical analysis and reproducible research in bioinformatics, to analyze and document the analysis of an example RNA-Seq data set from tomato pollen undergoing chronic heat stress. Also, we show how to use Integrated Genome Browser to visualize read coverage graphs for differentially expressed genes. Applying the protocol described here and using the provided data sets represent a useful first step toward building RNA-Seq data analysis expertise in a research group. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 7 | 17% |
| Germany | 2 | 5% |
| Netherlands | 2 | 5% |
| Sweden | 2 | 5% |
| United Kingdom | 2 | 5% |
| India | 1 | 2% |
| Italy | 1 | 2% |
| Norway | 1 | 2% |
| China | 1 | 2% |
| Other | 5 | 12% |
| Unknown | 17 | 41% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 24 | 59% |
| Members of the public | 17 | 41% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 3 | 1% |
| Chile | 2 | <1% |
| Italy | 2 | <1% |
| Germany | 1 | <1% |
| France | 1 | <1% |
| Brazil | 1 | <1% |
| Portugal | 1 | <1% |
| Denmark | 1 | <1% |
| Luxembourg | 1 | <1% |
| Other | 0 | 0% |
| Unknown | 238 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 71 | 28% |
| Researcher | 55 | 22% |
| Student > Master | 29 | 12% |
| Student > Bachelor | 17 | 7% |
| Student > Doctoral Student | 13 | 5% |
| Other | 30 | 12% |
| Unknown | 36 | 14% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 93 | 37% |
| Biochemistry, Genetics and Molecular Biology | 73 | 29% |
| Medicine and Dentistry | 12 | 5% |
| Computer Science | 6 | 2% |
| Immunology and Microbiology | 5 | 2% |
| Other | 24 | 10% |
| Unknown | 38 | 15% |