Code for He et al elife 2017 paper
This repository includes raw data and code for reproducing Figure 3A-D, 4B-D, 5B-C and figure supplements for 3 and 4 in the paper.
The repository is organized into two folders. Figure 3 and 4 are combined because they both use data obtained in the S. cerevisiae background. Figure 5 uses data obtained in the C. glabrata background.
Each folder contains one or more R Notebook files. Data used for plotting are stored in the "input" folder therein and the final figures are in "figure_output" folder.
Machine and software specifications
Running the code requires installation of the latest version of R and Rstudio. Below are the output of the session information used to generate all results in this repository.
> sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Yosemite 10.10.5 locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods  base other attached packages:  GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8  S4Vectors_0.8.11 edgeR_3.12.0 RColorBrewer_1.1-2  data.table_1.10.4 limma_3.26.8 NMF_0.20.6  Biobase_2.30.0 BiocGenerics_0.16.1 cluster_2.0.5  rngtools_1.2.4 pkgmaker_0.22 registry_0.3  plyr_1.8.4 cowplot_0.7.0 ggplot2_2.2.1 loaded via a namespace (and not attached):  Rcpp_0.12.10 XVector_0.10.0 knitr_1.16 magrittr_1.5  zlibbioc_1.16.0 doParallel_1.0.10 munsell_0.4.3 colorspace_1.2-6  xtable_1.8-2 gridBase_0.4-7 foreach_1.4.3 stringr_1.2.0  tools_3.3.2 grid_3.3.2 gtable_0.2.0 iterators_1.0.8  lazyeval_0.2.0 digest_0.6.9 tibble_1.3.0 reshape2_1.4.2  codetools_0.2-15 stringi_1.0-1 scales_0.4.1