Last updated: 2016-07-22
Code version: ad1ec8d74f4e5a35b272897297f72042324346f3
The following are examples of the implementation of the EDGE (Storey et al 2005) software to analyze comparative longitudinal time series RNA-seq data.
Wang X et al 2014 compares gene expression patterns in the hippocampus of one gene, Glud1 (Glutamate Dehydrogenas 1) in transgenic versus wild type mice. See Figure 6 for a nice output. Also see figures 1, 3, and 4 for hierarchical clustering of genes at different time points.
Li F et al 2015 used EDGE to identify differentially expressed lncRNAs as well as mRNAs across developmental states. The resulting curves can be found in 4b and 4c and some sample summaries are found in Figure 5 and Figure 6.
Scialdone et al 2016 uses a clustering method to perform expression profiling in single cell data e.g. Extended Data Figures 3, 6, and 9. Do you think that it’s worth talking about this?
sessionInfo()R Under development (unstable) (2016-03-11 r70310)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.13
loaded via a namespace (and not attached):
[1] magrittr_1.5 formatR_1.4 tools_3.3.0 htmltools_0.3.5
[5] yaml_2.1.13 Rcpp_0.12.5 stringi_1.1.1 rmarkdown_0.9.6
[9] stringr_1.0.0 digest_0.6.9 evaluate_0.9