These documents are a series of S.pyogenes TNSeq and RNASeq analyses.

TODO

  1. Rerun essentiality tools with these new alignments
  1. Include the results of that as annotation columns in the following experiments.

Experiments performed

In my more recent analyses I split the tasks into a few pages:

  1. preprocessing.html Tasks performed to make count tables.
  2. annotation.html Data shared by all experiments (annotations, genomes, etc).
  3. essentiality.html Steps performed to run essentiality.
  4. thyexpress.html RNASeq of wt during the growth curve, early/late/stationary.
  5. thytnseq.html The first TNSeq experiments in THY over time.
  6. thyrnatn.html Combine the TNSeq and RNASeq from #3/#4 above.
  7. subcu.html Subcutaneous infection over time in mice.
  8. pmnexp1.html Initial PMN infection with 1 day outgrowth.
  9. pmnexp2.html Following attempt of PMN infection with 4 hours outgrowth.
  10. abscess.html Rabbit abscess model with respect to time.
  11. rpoe.html RNASeq using an rpoE mutant and complementation strain.
  12. cpsy.html RNASeq using an cpsY mutant and friends in thy and plasma.
pander::pander(sessionInfo())

R version 3.3.1 (2016-06-21)

**Platform:** x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=en_US.UTF-8, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C

attached base packages: stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: hpgltools(v.2016.02)

loaded via a namespace (and not attached): Rcpp(v.0.12.7), digest(v.0.6.10), grid(v.3.3.1), plyr(v.1.8.4), gtable(v.0.2.0), formatR(v.1.2.1), magrittr(v.1.5), evaluate(v.0.9), scales(v.0.4.0), ggplot2(v.2.1.0), stringi(v.1.1.1), rmarkdown(v.1.0), tools(v.3.3.1), pander(v.0.6.0), stringr(v.1.1.0), munsell(v.0.4.3), yaml(v.2.1.13), colorspace(v.1.2-6), htmltools(v.0.3.5) and knitr(v.1.14)