S.cerevisiae 2016: RNAseq analyses.

1 Analyses of 4 S.cerevisiae strains, wt and mutant for pseudouridylation(CBF5), UPF1, and double.

The goal of this project is to look for changes in the yeast transcriptome as a result of a mutation(s) in CBF5, UPF1, and both. This document is intended to make it easier to reproduce/improve the analyses performed.

1. preprocessing.html The steps performed to preprocess the data.
2. annotation.html Data shared by all the downstream analyses.
3. sample_estimation.html Check the samples for suitability.
4. differential_expression.html Performing the DE analyses.
5. ontology.html Perform ontology searches.

2 TODO list

The following are some requests I have received and whether or not I think I did them:

• 2017-05-18
• Plot jacobson vs. wcmu/wcwu scatter plot
• Split old and new analyses and clean them up
• Plot old/new data scatter plot for cbf5

3 Finished TODO

• 2017-05-18
• Plot jacobson vs. wcmu/wcwu scatter plot – except something is wonky.

4 Installation and setup

These are rmarkdown documents which make heavy use of the hpgltools package. The following section demonstrates how to set that up in a clean R environment.

## Use R's install.packages to install devtools.
install.packages("devtools")
## Use devtools to install hpgltools.
devtools::install_github("abelew/hpgltools")
## Load hpgltools into the R environment.
library(hpgltools)

library('pander')
pander(sessionInfo())

R version 3.4.4 (2018-03-15)

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

locale: LC_CTYPE=en_US.utf8, LC_NUMERIC=C, LC_TIME=en_US.utf8, LC_COLLATE=en_US.utf8, LC_MONETARY=en_US.utf8, LC_MESSAGES=en_US.utf8, LC_PAPER=en_US.utf8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.utf8 and LC_IDENTIFICATION=C

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

other attached packages: pander(v.0.6.1) and hpgltools(v.2018.03)

loaded via a namespace (and not attached): Rcpp(v.0.12.16), xml2(v.1.2.0), roxygen2(v.6.0.1), knitr(v.1.20), magrittr(v.1.5), devtools(v.1.13.5), BiocGenerics(v.0.24.0), munsell(v.0.4.3), colorspace(v.1.3-2), R6(v.2.2.2), rlang(v.0.2.0), foreach(v.1.4.4), plyr(v.1.8.4), stringr(v.1.3.0), tools(v.3.4.4), parallel(v.3.4.4), grid(v.3.4.4), Biobase(v.2.38.0), data.table(v.1.10.4-3), gtable(v.0.2.0), withr(v.2.1.2), commonmark(v.1.4), htmltools(v.0.3.6), iterators(v.1.0.9), lazyeval(v.0.2.1), yaml(v.2.1.18), rprojroot(v.1.3-2), digest(v.0.6.15), tibble(v.1.4.2), ggplot2(v.2.2.1), base64enc(v.0.1-3), codetools(v.0.2-15), memoise(v.1.1.0), evaluate(v.0.10.1), rmarkdown(v.1.9), stringi(v.1.1.7), pillar(v.1.2.1), compiler(v.3.4.4), scales(v.0.5.0) and backports(v.1.1.2)