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title: "Big Data Biology: Workshop material"
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[back to Big Data Biology main page](http://www-users.york.ac.uk/~dj757/BIO00047I/BIO00047I_index.html)


#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.

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**You should decide which data set you will use for your project after workshop 3.** </br>
All the data sets are is described in detail  [here](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/BIO00047I-data-description-2021.pdf).

**Then:** start to work on data analysis in your own time. See more details about the assessment on the [VLE](https://vle.york.ac.uk/webapps/blackboard/execute/announcement?method=search&context=course&course_id=_88160_1).

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

***

##Fungal Ecology Dataset

[**Workshop 1**](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day1_open.html)<br>
Keywords:read.csv,rownames,which,colSums,barplot,write.table<br>

[**Workshop 2**](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day2_open.html)</br>
Keywords:splitting text,as.character,strsplit,sapply,for loop,OTUs,phylum</br>

[**Workshop 3**](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day3_open.html)<br>
Keywords:<br>

[**Workshop 4**](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day4_open.html)<br>
Keywords:<br>


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##Fission Yeast Dataset

**Get the data** as an Rda file [here](http://www-users.york.ac.uk/~dj757/BIO00047I/data/fission_yeast_data.2018-11-21.Rda).

[**Workshop 1**](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop1B.html)<br>
Keywords:nrow,ncol,load,hist,log10<br>

[**Workshop 2**](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop2B.html)<br>
Keywords:box and whiskers plot,subset,essential gene,cor.test,wilcox.test</br>

[**Workshop 3**](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop3B.html)<br>
Keywords:<br>

[**Workshop 4**](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop4B.html)<br>
Keywords:<br>

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##Brassica Dataset

[**Workshop 1**](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data.html)<br>
Keywords:dim,rownames,is.numeric,write.table,save.image,rm,subset<br>

[**Workshop 2**](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data2.html)</br>
Keywords:read.delim,transpose,linear model,anova,as.data.frame,for loop

[**Workshop 3**](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data3.html)</br>
Keywords:read.delim,transpose,linear model,anova,as.data.frame,for loop

[**Workshop 4**](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data4.html)<br>
Keywords:<br>

***

##Crocodile Macroevolution Dataset

**Get the data** as a zip archive [here](http://www-users.york.ac.uk/~dj757/BIO00047I/data/all-crocodile-data.zip), or as files [here](https://www-users.york.ac.uk/~kd856/WorkshopData/).

[**Workshop 1**](https://www-users.york.ac.uk/~kd856/Workshop1_Rmarkdown.html)<br>
Keywords:read.csv,head,smooth,plot<br>

[**Workshop 2**](https://www-users.york.ac.uk/~kd856/Workshop2_Rmarkdown.html)</br>
Keywords:library(BAMMtools),library(phytools),library(strap),read.tree,phylogenetic,phylogeny</br>

[**Workshop 3**](https://www-users.york.ac.uk/~kd856/Workshop3_Rmarkdown.html)</br>
Keywords:library(BAMMtools),library(phytools),library(strap),read.tree,phylogenetic,phylogeny</br>

[**Workshop 4**](https://www-users.york.ac.uk/~kd856/Workshop4_Rmarkdown.html)</br>
Keywords:


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##Workshop 5: report writing

Workshop 5 is a report writing tutorial. See [here](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop5.html)

***


**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](http://www-users.york.ac.uk/~er13/17C%20-%202018/BIO00017C.html) . These will be useful for reminding yourself what you know about R. There are also some suggestions on the VLE.



