RNAseq of Saccharomyces cerevisiae strains.

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:

3 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 3.3.3 (2017-03-06)

**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: stats4, parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: hpgltools(v.2017.01), ruv(v.0.9.6), pander(v.0.6.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene(v.3.2.2), GenomicFeatures(v.1.26.4), GenomicRanges(v.1.26.4), GenomeInfoDb(v.1.10.3), BiocInstaller(v.1.24.0), AnnotationDbi(v.1.36.2), IRanges(v.2.8.2), S4Vectors(v.0.12.2), Biobase(v.2.34.0), AnnotationHub(v.2.6.5) and BiocGenerics(v.0.20.0)

loaded via a namespace (and not attached): nlme(v.3.1-131), bitops(v.1.0-6), matrixStats(v.0.52.2), devtools(v.1.13.1), RColorBrewer(v.1.1-2), httr(v.1.2.1), rprojroot(v.1.2), tools(v.3.3.3), backports(v.1.0.5), R6(v.2.2.1), DBI(v.0.6-1), lazyeval(v.0.2.0), mgcv(v.1.8-17), colorspace(v.1.3-2), withr(v.1.0.2), curl(v.2.6), compiler(v.3.3.3), preprocessCore(v.1.36.0), xml2(v.1.1.1), rtracklayer(v.1.34.2), labeling(v.0.3), scales(v.0.4.1), genefilter(v.1.56.0), commonmark(v.1.2), stringr(v.1.2.0), digest(v.0.6.12), Rsamtools(v.1.26.2), rmarkdown(v.1.5), XVector(v.0.14.1), base64enc(v.0.1-3), htmltools(v.0.3.6), limma(v.3.30.13), RSQLite(v.1.1-2), shiny(v.1.0.3), BiocParallel(v.1.8.2), gtools(v.3.5.0), dplyr(v.0.5.0), RCurl(v.1.95-4.8), magrittr(v.1.5), GO.db(v.3.4.0), Matrix(v.1.2-10), Rcpp(v.0.12.10), munsell(v.0.4.3), stringi(v.1.1.5), yaml(v.2.1.14), edgeR(v.3.16.5), SummarizedExperiment(v.1.4.0), zlibbioc(v.1.20.0), plyr(v.1.8.4), grid(v.3.3.3), ggrepel(v.0.6.5), crayon(v.1.3.2), lattice(v.0.20-35), Biostrings(v.2.42.1), splines(v.3.3.3), annotate(v.1.52.1), locfit(v.1.5-9.1), knitr(v.1.15.1), corpcor(v.1.6.9), reshape2(v.1.4.2), codetools(v.0.2-15), biomaRt(v.2.30.0), XML(v.3.98-1.7), evaluate(v.0.10), data.table(v.1.10.4), httpuv(v.1.3.3), foreach(v.1.4.3), testthat(v.1.0.2), gtable(v.0.2.0), assertthat(v.0.2.0), ggplot2(v.2.2.1), openxlsx(v.4.0.17), mime(v.0.5), xtable(v.1.8-2), roxygen2(v.6.0.1), survival(v.2.41-3), tibble(v.1.3.0), iterators(v.1.0.8), GenomicAlignments(v.1.10.1), memoise(v.1.1.0), sva(v.3.22.0) and interactiveDisplayBase(v.1.12.0)