• Manuals

Browse the manual

• Introduction to the Advanced RNA-Seq plugin
  • Input data and normalization
    • Normalization
    • Metadata
  • PCA for RNA-Seq
    • Principal component analysis plot (2D)
    • Principal component analysis plot (3D)
  • Differential Expression for RNA-Seq
    • The statistical model
    • Output of the Differential Expression for RNA-Seqtool
    • Statistical comparison tracks
    • The volcano plot
  • Create Heat Map for RNA-Seq
    • Clustering of features and samples
    • The heat map view
  • Create Expression Browser
    • The expression browser
  • Create Venn Diagram for RNA-Seq
    • Venn diagram table view
• Installation of the Advanced RNA-Seq plugin
• Uninstall
• Bibliography

Bibliography

Auer and Doerge, 2010

Auer, P. L. and Doerge, R. (2010).
Statistical design and analysis of rna sequencing data.
Genetics, 185(2):405-416.

Mortazavi et al., 2008

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008).
Mapping and quantifying mammalian transcriptomes by rna-seq.
Nat Methods, 5(7):621-628.

Robinson et al., 2010

Robinson, M. D., McCarthy, D. J., and Smyth, G. K. (2010).
edger: a bioconductor package for differential expression analysis of digital gene expression data.
Bioinformatics, 26(1):139-140.

Robinson and Oshlack, 2010

Robinson, M. D. and Oshlack, A. (2010).
A scaling normalization method for differential expression analysis of RNA-seq data.
Genome Biol., 11(3):R25.

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