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

***

<span style="color: purple"> <font size="4">**You don't need to watch all these videos urgently.** See the week by week guide in the VLE for a gentle video-watching schedule. New concepts take time to learn, so be patient with yourself. :-)</span></font>

***
We include video guides to the workshops. Use these if you need some extra guidance, after the live workshop.

***
#Lectures and module info

##Lecture 1
[**Lecture 1 video (Part A)**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=0f1757f1-b3df-4695-a330-ae1b00c391bc) | 35 minutes</br>
Introduction to big data biology concepts. Introduction to high-throughput methods.</br></br>
[**Lecture 1 video (Part B)**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=72254c02-8401-4ad1-8ded-ae1b00c3917d) | 18 minutes</br>
Outline of the module. How we teach, and what you need to do.</br>

Download as [PDF](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture1.pdf) | [Powerpoint](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture1.pptx)</br>


##Lecture 2 
[**Lecture 2 video**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=4562d447-eec1-4608-9ea7-ae1b00c37300&query=lecture%202) | 34 minutes</br>

Download as [PDF](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture2.pdf) | [Powerpoint](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture2.pptx) 


***

#R Studio Skills

[**Installing R and R studio**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=dc135264-8750-44f6-b517-ae1b00c3911b) | 9 minutes</br>
[Website to download R Studio](https://rstudio.com/products/rstudio/download/)</br>
Keywords: R studio, packages, tidyverse, install.packages(), library()</br>

[**Loading data and saving data in R**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=54c82bc8-e153-4913-9e18-ae1b00c34d2f) | 10 minutes</br>
Keywords: read.table, read.delim, save.image, load</br>


[**walkthrough of ggplot2**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=81d6c863-5c46-4afe-9e86-ae1b00c34972)| 26 minutes</br>
See also [data-to-viz.com](https://www.data-to-viz.com/) to find out what plot may suit your data.
Keywords:tidyverse, ggplot2, geom_histogram, geom_density, geom_violin, geom_boxplot, stat_compare_means</br>


[**Making plots in R**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=a3080a6c-64d5-4e8b-a6c4-ae1b00c39036) | 17 minutes</br>
[See the R commands.](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/plots-in-R.R)</br>
Keywords: boxplot, scatterplot, barplot, box and whiskers plot, histogram, hist, stripchart, summary, head</br>

[**Data types in R**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=55ef5e77-61dd-4a92-8675-ae1b00c374f9) | 13 minutes</br>
**Explains** data types in R (strings, characters, numeric, Booleans).</br>
Keywords: variables, case-sensitive, TRUE/FALSE, strings, characters, numeric, Boolean(TRUE/FALSE), substring, paste, sub, max, min, abs, and (&), or (|), factors, as.character, as.numeric</br>

[**Data structures in R**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=dc277ce9-0594-4700-85da-ae1b00c3742e) | 13 minutes</br>
**Explains** vectors, data frames, matrices (matrix), lists and how to use them.</br>
Keywords:table, list, read.table, data.frame, column names, matrix, matrices, vector, list, dim, names</br>

[**What is a function?**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=87e2e200-6add-4689-8fef-ae1b00c35057) | 7 minutes </br>
Keywords: Apply, Sapply, lapply</br>

[**Apply and Sapply**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=c70e2289-f829-4c3f-aad0-ae1b00c34ff9) | 15 minutes</br>
Keywords: Apply, Sapply, applying a function to rows or columns of a matrix

***
*Feel free to use and/or modify any R code on this website.*

***

#Data Analysis Concepts

[**R tools to summarise large data sets**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=431d63ef-4132-4bb4-875b-ae1b00c34a2c) | 30 minutes</br>
Keywords: summary, mean, median, nrow, ncol, dim, subset, hist, head, tail</br>
R code is [here](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/tools-to-summarise.R)</br>

[**Multiple test correction**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=ea04a0e9-1b64-40b3-8fde-ae1b00c3713a)</br>
Keywords: Bonferroni 

[**Exploring data with plots and summaries**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=27a59a4d-4e00-41f8-9855-ae1b00c38ff4) | 12 minutes </br>
[See the R commands.](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/exploring-data.R)</br>
Keywords: correlation, mean, median, summary, hist, plot, log scale, log10

[**Correlation is not causation**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=e2a746f6-8470-4880-a5ed-ae1b00c34cf0) | 7 minutes </br>
Keywords:pirates, ice cream, sharks, correlation, causation, cor.test, crocodilians

[**Linear models**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=ea04a0e9-1b64-40b3-8fde-ae1b00c3713a) | 9 minutes </br>
Keywords: gradient, intercept, lm, glucosinolates, F-test, Brassica

***

#Workshop video guides
***

**Please note:** not all these workshop videos will be available at the start of term. We'll upload them before you need them though.  

***

##Fungal Ecology Dataset

[**Introduction to the Fungal Ecology Dataset**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=f51d7e94-63e5-480c-8d82-ae1b00c37872) | 11 minutes</br>
Keywords: Daphne Ezer, ecology, soil</br>

[**Workshop 1** (part 1)](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=ca63c6ec-257c-4c73-8e94-ae1b00c37783) | 9 minutes</br>
Keywords:fungi, ecology, metagenomics, operational taxonomic units (OTUs), read.csv, dim, class</br>

[**Workshop 1** (part 2)](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=31edd3be-765a-465b-a0ee-ae1b00c37699) | 14 minutes</br>
Keywords:fungi, ecology, metagenomics, rownames, colnames, ecology, hist, histogram, which, colSums, barplot</br>

[**Workshop 1** (part 3, optional)](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=832fd65b-8768-41d5-94a4-ae1b00c37556) | 12 minutes</br>
Keywords:grep, logical functions, which, TRUE, FALSE, sort, table</br>

[**Workshop 2** (part 1)](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=11d8a253-1272-4f9d-afb9-ae1b00c34fb3) | 15 minutes</br>
Keywords:which, grep, load, sapply</br>

[**Workshop 2** (part 2)](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=fd85eb7f-a61a-4987-9c7b-ae1b00c34e46) | 16 minutes</br>
Keywords:sapply, unique, missing data, library(seqinr), write.fasta, save.image</br>

[**Workshop 3**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=a90b5e78-a300-4635-87c8-ae1b00c34ddb) | 20 minutes</br>
Keywords:dim, sum, barplot, plot, technical artifacts, rainbow colour palette, length, legend, order, Chi-squared test, chisq.test, library(MASS) </br>

[**Workshop 4**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=221e901f-9930-4d94-ab37-ae1b00c34d97) | 20 minutes</br>
Keywords: fungal diversity, load, as.numeric, unique, pie chart, library(Rgraphviz), Simpson's Index of Diversity, ANOVA test</br>




***

##Fission Yeast Dataset

[**Introduction to the Yeast Dataset**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=3e9cbbfc-ef8c-4c2c-97b3-ae1b00c372bf) | 7 minutes </br>
Keywords: Fission yeast, Schizosaccharomyces pombe, Daniel Jeffares, essential genes, Pombase, Angeli, gene expression, mRNA half life, protein copies/cell</br>

[**Workshop 1**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=4d749774-74e9-43d5-8b86-ae1b00c37271) | 25 minutes </br>
Keywords: setwd, rm, hist, load, subset, nrow, ncol, summary, log10, pdf</br>

[**Workshop 2**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=be8357e8-17ff-4345-bd68-ae1b00c37235) | 24 minutes</br>
Keywords:  box and whiskers plot, boxplot, wilcox.test, log10, mRNA copies per cell, essential genes</br>

[**Workshop 3**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=c3324c6f-7151-4a3e-b6e1-ae1b00c371d9) | 38 minutes</br>
Keywords: ggplot2, transposon, merge</br>

[**Workshop 4**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=98b6df09-6709-4db2-a626-ae1b00c37196) | 34 minutes</br>
Keywords:  conservation, phyloP, bar plot, matrix, chisq.test, figure legend</br>

***

##Brassica Dataset

[**Introduction to the Brassica Dataset**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=69f1df55-1182-4a4a-8bdc-ae1b00c3921a) | 11 minutes </br>
Keywords: Brassica, Andrea Harper, Oilseed rape, RPKM, RNAseq, glucosinolate</br>

[**Workshop 1**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=89da8915-372f-4948-ad39-ae1b00c37398) | 22 minutes </br>
Keywords:read.delim, dim, class, Brassica, rownames, OSR101_RPKM2[,-1], using square brackets, [],  is.numeric, sapply, hist, is.numeric, row.names, rowmeans, subset, RPKM, summary, write.table, barplot, save.image</br>

[**Workshop 2**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=b32c7b7f-12b7-4c38-ac16-ae1b00c35134) | 24 minutes</br>
Keywords:read.table, read.delim, rownames, "for" loops, OSR_merge[1:5.1:5], paste, linear model, lm, abline, line of best fit, anova, coefficients, summary, as.data.frame, ncol</br>

[**Workshop 3**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=aacd25a9-6cf2-42cc-8dd5-ae1b00c34bcd) | 26 minutes </br>
Keywords:qqnorm, qqline, read.delim, library("car"), qqPlot, results$P.value, merge (to merge data frames), order, library(ggplot2), geom_point, theme_classic, -log10, Bonferroni multiple test correction, gl, false discovery rate, FDR, colnames</br>

[**Workshop 4**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=2ca65e5e-88bf-4f7f-be5c-ae1b00c34b66) | 16 minutes </br>
Keywords: read.delim, NCBI Blast, stringsAsFactors, rownames </br>

***

##Pseudosuchia (crocodile) Macroevolution Dataset

[**Introduction to the Crocodile Macroevolution Dataset**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=dc0bd9f1-c1d0-4864-a298-ae1b00c37100)</br>
Keywords: Katie Davis, evolution, phylogeny</br>

[**Workshop 1**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=d04a9015-7fef-41a8-9b27-ae1b00c34b24) | 27 minutes </br>
Keywords:macroevolution, pseudosuchia, global climate change, read.csv, dim, class, plot, xlim, sea level, save.image

[**Workshop 2**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=1e86120a-f156-4c0c-a2ae-ae1b00c34ad4) | 28 minutes </br>
Keywords:macroevolution, pseudosuchia, global climate change, read.csv, dim, class, plot, xlim, sea level, save.image

[**Workshop 3**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=80186c68-4405-4b44-bac6-ae1b00c32a41) | 17 minutes </br>
Keywords:macroevolution, pseudosuchia, loading libraries, BAMMtools, Bayesian, phylogeny, phylogenetic trees, speciation, plotRateThroughTime

[**Workshop 4**](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=4d578f06-105d-49cf-8e9f-ae1b00cc3898) | 26 minutes </br>
Keywords:ggplot2, Detrended Cross Correlation Analysis, 

***

##Report Writing

[**Workshop 5:** Report Writing Guide](https://york.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=c390e5ab-73aa-4ca1-a0d6-ae1b00c37359) | 38 minutes</br>

***


