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Workshop material

Keywords! All the workshops and videos have lists of keywords beneath them. If you want to find workshops that an an R function, or understand a new concept, search the keywords.

You should decide which data set you will use for your project after workshop 3.
All the data sets are is described in detail here.

Then: start to work on data analysis in your own time. See more details about the assessment on the VLE.

The assessment is due after Easter: by 22nd April 2021 (no later than 11am).

Fungal Ecology Dataset

Workshop 1
Keywords:read.csv,rownames,which,colSums,barplot,write.table

Workshop 2
Keywords:splitting text,as.character,strsplit,sapply,for loop,OTUs,phylum

Workshop 3
Keywords:

Workshop 4
Keywords:

Fission Yeast Dataset

Get the data as an Rda file here.

Workshop 1
Keywords:nrow,ncol,load,hist,log10

Workshop 2
Keywords:box and whiskers plot,subset,essential gene,cor.test,wilcox.test

Workshop 3
Keywords:

Workshop 4
Keywords:

Brassica Dataset

Workshop 1
Keywords:dim,rownames,is.numeric,write.table,save.image,rm,subset

Workshop 2
Keywords:read.delim,transpose,linear model,anova,as.data.frame,for loop

Workshop 3
Keywords:read.delim,transpose,linear model,anova,as.data.frame,for loop

Workshop 4
Keywords:

Crocodile Macroevolution Dataset

Get the data as a zip archive here, or as files here.

Workshop 1
Keywords:read.csv,head,smooth,plot

Workshop 2
Keywords:library(BAMMtools),library(phytools),library(strap),read.tree,phylogenetic,phylogeny

Workshop 3
Keywords:library(BAMMtools),library(phytools),library(strap),read.tree,phylogenetic,phylogeny

Workshop 4
Keywords:

Workshop 5: report writing

Workshop 5 is a report writing tutorial. See here

Credits.

  • The Brassica workshops were written by Andrea Harper, using data from her own ressearch.

  • The fission yeast workshops were written by Daniel Jeffares, using data from Angeli/his own ressearch.

  • Fungal metagenomic workshops were written by Daphne Ezer, using data from Thorunn Helgasson.

  • The Pseudosuchia macroevolution workshops were written by Katie Davis, using data from her own ressearch.

  • Big thanks to Emma Rand for showing us how to use R Markdown to make this site. Thanks Emma! You can see Emma's R workshops from 1st year: BIO00017C . These will be useful for reminding yourself what you know about R. There are also some suggestions on the VLE.