A collection of scripts and files used whilst bioinformagicianing
BioNetwork_2.R - A script to produce a network graph of the MCRI bioinformatics collaborations with other groups based on a google docs spreadsheet.
DEXY.R - A script to extract Differential Exon Usage using DexSeq from a counts matrix (rows exons, columns samples) then summarised to per gene q values.
DIY.html - An html file (based on a Rmarkdown Rstudio notebook) which is a tutorial on how make your own ALL classifier, in this example i base the classifier of a simulated dataset.
ClassifierBuilder.ipynb - A python notebook which is a tutorial on how make your own ALL classifier, in this example i base the classifier of a smulated dataset.
Diff_Ex_Skeleton.Rmd - A cheeky R markdown skeleton i made for a standard Differential Expression RNA seq analysis, this was made in the early days so it probably isn't that advanced.
Expression Outliers.R - A quick script i made to explore Expression Outliers for various interesting genes in the ALL samples we though were more unusual from the MCRI cohort.
Express Yourself - My first ever shiny app for looking into expression outliers as a web app instead of statically as in the above script.
Making_AllSorts.Rmd - A script to make the AllSorts Classifier (really messy, not cleaned)
Making_AllSorts.html - A script to make the AllSorts Classifier (to view it, preview the html on: https://rawgit.com/Quarkins/Bioinformatics-Tidbits/master/Making_AllSorts.html
Combined Dec2016 - A script which combines all the counts and target data of samples measured at MCRI and then classifies them and constructs RData objects used by the Express Yourself R Shiny App
MakeSashimi.R - A little script used by the ST paper in order to make a sashimi style plot using GViz.
varCalling.sh - A script to run the standard rna seq GATK variant calling pipeline on a superTranscriptome. This (or a variant of this) was used for the ST paper.
BashSTPaperCommands.sh - A bunch of bash and command line instructions for running various miscellaneous steps of the ST paper annalysis.