Tools for expression based analyses of microorganisms
- clustering
- regulatory motif discovery
- sequence search
- exploratory analysis workflow capture
Coding conventions:
- env global in RData output has the main data items for a study
- globals use . as word separator, e.g. env$meme.data
Dependencies:
- MEME, 4.10.2 (important!)
- R
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
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] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] MASS_7.3-37 flexclust_1.3-4 modeltools_0.2-21 lattice_0.20-29
[5] shinyBS_0.50 shiny_0.11.0.9001
loaded via a namespace (and not attached):
[1] BiocGenerics_0.12.1 digest_0.6.8 GenomeInfoDb_1.2.4
[4] GenomicRanges_1.18.4 htmltools_0.2.6 httpuv_1.3.2
[7] IRanges_2.0.1 mime_0.2 parallel_3.1.2
[10] R6_2.0.1 Rcpp_0.11.3 S4Vectors_0.4.0
[13] xtable_1.7-4 XVector_0.6.0