Please follow the instructions under Get Data and Core Software headings below. Depending on the class you’re taking, you may also need to follow additional setup instructions under the Electives heading.
Click the Data link on the navbar at the top. You can download all the data needed by downloading this zip file or by downloading individual data sets as needed at the Data page.
Install the following software regardless of which class(es) you’re taking.
Install R. You’ll need R version 3.5.0 or higher.1 Download and install R for Windows or Mac (download the latest R-3.x.x.pkg file for your appropriate version of Mac OS).
Download and install RStudio Desktop version >= 1.1.456.
R and RStudio are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment that makes using R much easier. You need R installed before you install RStudio.
We will need to install several core packages needed for most lessons. Launch RStudio (RStudio, not R itself). Ensure that you have internet access, then copy and paste the following commands, one-at-a-time, into the Console panel (usually the lower-left panel, by default) and hit the Enter/Return key. If you receive an error message when trying to install any particular package, please make note of which one you had trouble with, and email one of the instructors prior to class with the command you typed and the error you received.
install.packages("dplyr")
install.packages("readr")
install.packages("tidyr")
install.packages("ggplot2")A few notes:
Check that you’ve installed everything correctly by closing and reopening RStudio and entering the following command at the console window (don’t worry about any messages that look something like the following objects are masked from ...3, or Warning message: package ... was build under R version ...4):
library(dplyr)
library(readr)
library(tidyr)
library(ggplot2)This may produce some notes or other output, but as long as you don’t get an error message, you’re good to go. If you get a message that says something like: Error in library(somePackageName) : there is no package called 'somePackageName', then the required packages did not install correctly. Please do not hesitate to email one of the instructors prior to class if you are still having difficulty. In this email, please copy and paste what you typed in the console, and all of the output that streams by in the console.
For our refresher course on tidy data and exploratory data analysis, we’ll need additional packages from the tidyverse suite of packages, as well as a few additional packages. A quick note on the tidyverse package (https://www.tidyverse.org/): the tidyverse is a collection of other packages that are often used together. When you install or load tidyverse, you also install and load all the packages that we’ve used previously: dplyr, tidyr, ggplot2, as well as several others. Because we’ll be using so many different packages from the tidyverse collection, it’s more efficient load this “meta-package” rather than loading each individual package separately. Install these packages. You’ll need all four.
install.packages("tidyverse")
install.packages("ggrepel")
install.packages("scales")
install.packages("lubridate")I’ll demonstrate some functionality from these other packages as well. They’re handy to have installed, but are not strictly required.
install.packages("plotly")
install.packages("DT")To ensure you have all these packages installed correctly, try loading them all with library().
## Required packages:
library(tidyverse)
library(ggrepel)
library(scales)
library(lubridate)
# Optional packages
library(plotly)
library(DT)You may get some red message text, but if you see an error message, something along the lines of Error in library(packageName) : there is no package called 'packageName', then the package that raised that error did not install correctly.
The instructions below apply to additional “elective” classes, and are not strictly required as part of the core set of classes. Install these as necessary.
Several additional setup steps required for the reproducible research with RMarkdown class.
install.packages("knitr")
install.packages("rmarkdown")knitr, yaml, htmltools, caTools, bitops, rmarkdown, and maybe a few others). Click “Yes” to install these.Install the core Bioconductor packages (more information here). These packages are installed differently than “regular” R packages from CRAN. Copy and paste these lines of code into your R console one at a time.
source("http://bioconductor.org/biocLite.R")
biocLite()A few notes:
n at the prompt at hit enter.n for no, and hit enter.Check that you’ve installed everything correctly by closing and reopening RStudio and entering the following command at the console window:
library(BiocInstaller)If you get a message that says something like: Error in library(BiocInstaller) : there is no package called 'BiocInstaller', then the required packages did not install correctly. Please do not hesitate to email one of the instructors prior to the course if you are still having difficulty. In this email, please copy and paste what you typed in the console, and all of the output that streams by in the console.
Prerequisites! This is not an introductory R class. This lesson assumes a basic familiarity with R, data frames, and to a lesser degree, manipulating data with dplyr and %>%, and data visualization with ggplot2.
Software setup: Follow instructions above for R+RStudio+Packages, CRAN packages, and Bioconductor. See the sections above for full instructions and troubleshooting tips.
For this class you’ll also need the survminer package from CRAN and the and RTCGA, RTCGA.clinical, RTCGA.mRNA, packages from Bioconductor.
If you receive an error message when trying to install any particular package, please make note of which one you had trouble with, and email one of the instructors prior to class with the command you typed and the error you received.
# Install core CRAN packages:
install.packages("dplyr")
install.packages("readr")
install.packages("tidyr")
install.packages("ggplot2")
# For this class, also install survminer from CRAN
install.packages("survminer")
# Install Bioconductor core packages:
install.packages("BiocManager")
# For this class, you'll also need RTCGA and RTCGA data packages
BiocManager::install("RTCGA")
BiocManager::install("RTCGA.clinical")
BiocManager::install("RTCGA.mRNA")Check that you’ve installed everything correctly by closing and reopening RStudio and entering the following commands one-at-a-time in the console pane:
# Test CRAN package installation:
library(dplyr)
library(readr)
library(tidyr)
library(ggplot2)
# Test survminer
library(survminer)
# Test RTCGA:
library(RTCGA)
library(RTCGA.clinical)
library(RTCGA.mRNA)This may produce some notes or other output, but as long as you don’t get an error message, you’re good to go. If you get a message that says something like: Error in library(somePackageName) : there is no package called 'somePackageName', then the required packages did not install correctly. Please do not hesitate to email me prior to class if you are still having difficulty. In this email, please copy and paste what you typed in the console, and all of the output that streams by in the console.
Prerequisites! This is not an introductory R class. In addition to familiarity with R, this lesson also assumes familiarity with:
%>%Some knowledge of statistics and resampling procedures is helpful, but not strictly required.
Software setup: Follow instructions above for R+RStudio+Packages and CRAN packages. For this class, you’ll also need several additional packages described below. If you receive an error message when trying to install any particular package, please make note of which one you had trouble with, and email me prior to class with the command you typed and the error you received.
First, install the caret package, which provides a unified interface to hundreds of data mining and machine learning algorithms and a framework for model training and evaluation. This command will also install all the additional packages that caret recommends. You will also need to install a few other packages that are required by caret that might not be automatically installed. These are also listed below.
install.packages("caret", dependencies = c("Depends", "Suggests"))
install.packages("ModelMetrics")
install.packages("generics")
install.packages("gower")When you do this, you may get a note asking you about installing source packages that need compilation. If you get this message, focus on the console pane by clicking and type n and hit Enter at the prompt for “no.”
There are binary versions available but the source versions are later:
binary source needs_compilation
somePackage1 .... .... TRUE
somePackage1 .... .... FALSE
Do you want to install from sources the package which needs compilation?Similarly, if you get a message that looks like this, type n and hit Enter for “no.”
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘Rpoppler’ ‘Rmpi’
Do you want to attempt to install these from sources?The caret package provides the utilities for interfacing with many other packages’ machine learning algorithms. We’re going to fit models using Random Forest, stochastic gradient boosting, k-Nearest Neighbors, Lasso and Elastic-Net Regularized Generalized Linear Models. These require the packages randomForest, gbm, kknn, and glmnet, respectively. We will also need the mice package for multiple imputation. The following commands will install these packages.
install.packages("randomForest")
install.packages("gbm")
install.packages("kknn")
install.packages("glmnet")
install.packages("mice")Finally, we’ll conclude with a demonstration of forecasting, for which we’ll need the prophet package.
install.packages("prophet")Check that you’ve installed everything correctly by closing and reopening RStudio and entering the following commands one-at-a-time in the console pane. If you get an error telling you that the package isn’t installed, try re-installing it as demonstrated above. If you’re still having trouble, email me prior to class with the command you typed to install and the error(s) you received.
library(caret)
library(randomForest)
library(gbm)
library(kknn)
library(glmnet)
library(mice)
library(prophet)Download data we’ll use in class. You will need the following datasets from the data page:
Recommended reading prior to class:
(check back later)
Prerequisites! This is not an introductory R class. In addition to familiarity with R, this lesson also assumes familiarity with:
%>%Software setup: For this class, you’ll need R >= 3.5.0, and several additional packages described below. If you receive an error message when trying to install any particular package, please make note of which one you had trouble with, and email me prior to class with the command you typed and the error you received. If you’re not sure which version of R you’re using, run the sessionInfo() command to check. You must use >= 3.5.0 (3.4.x will not work).
install.packages("tidyverse")
install.packages("tidytext")
install.packages("gutenbergr")
install.packages("tm")
install.packages("topicmodels")To check that these are correctly installed, first close RStudio and then reopen it and run the following:
library(tidyverse)
library(tidytext)
library(gutenbergr)
library(tm)
library(topicmodels)Download the austen.csv data we’ll use in class from the data page.
Prerequisites! This is not an introductory R class. This lesson assumes a basic familiarity with R, data frames, manipulating data with dplyr and %>%, and data visualization with ggplot2.
Software setup: Follow instructions above for R+RStudio+Packages, CRAN packages, and Bioconductor. See the sections above for full instructions and troubleshooting tips.
For this class you’ll also need the DESeq2 package.
If you receive an error message when trying to install any particular package, please make note of which one you had trouble with, and email one of the instructors prior to class with the command you typed and the error you received.
# Install core CRAN packages:
install.packages("dplyr")
install.packages("readr")
install.packages("tidyr")
install.packages("ggplot2")
# Install Bioconductor core packages:
install.packages("BiocManager")
BiocManager::install()
# For this class, you'll also need DESeq2:
BiocManager::install("DESeq2")Check that you’ve installed everything correctly by closing and reopening RStudio and entering the following commands one-at-a-time in the console pane:
# Test CRAN package installation:
library(dplyr)
library(readr)
library(tidyr)
library(ggplot2)
# Test DESeq2 installation:
library(DESeq2)This may produce some notes or other output, but as long as you don’t get an error message, you’re good to go. If you get a message that says something like: Error in library(somePackageName) : there is no package called 'somePackageName', then the required packages did not install correctly. Please do not hesitate to email one of the instructors prior to class if you are still having difficulty. In this email, please copy and paste what you typed in the console, and all of the output that streams by in the console.
Download data we’ll use in class. Create a new folder somewhere on your computer that’s easy to get to (e.g., your Desktop). Name it bioconnector. Inside that folder, make a folder called data, all lowercase. Download the 3 data files below, saving them to the new bioconnector/data folder you just made.
countData): airway_scaledcounts.csvcolData): airway_metadata.csvRecommended reading prior to class:
Prerequisites! This is not an introductory R class. This lesson assumes a basic familiarity with R, data frames, manipulating data with dplyr and %>%, and most importantly, data visualization with ggplot2.
Software setup: Follow instructions above for R+RStudio+Packages, CRAN packages, and Bioconductor. See the sections above for full instructions and troubleshooting tips.
For this class you’ll also need the ggtree and Biostrings packages from Bioconductor.
If you receive an error message when trying to install any particular package, please make note of which one you had trouble with, and email one of the instructors prior to class with the command you typed and the error you received.
# Install core CRAN packages:
install.packages("dplyr")
install.packages("readr")
install.packages("tidyr")
install.packages("ggplot2")
# Install Bioconductor core packages:
source("http://bioconductor.org/biocLite.R")
biocLite()
# For this class, you'll also need ggtree and Biostrings:
biocLite("ggtree")
biocLite("Biostrings")Check that you’ve installed everything correctly by closing and reopening RStudio and entering the following commands one-at-a-time in the console pane:
# Test CRAN package installation:
library(dplyr)
library(readr)
library(tidyr)
library(ggplot2)
# Test ggtree and Biostrings installation:
library(ggtree)
library(Biostrings)This may produce some notes or other output, but as long as you don’t get an error message, you’re good to go. If you get a message that says something like: Error in library(somePackageName) : there is no package called 'somePackageName', then the required packages did not install correctly. Please do not hesitate to email one of the instructors prior to class if you are still having difficulty. In this email, please copy and paste what you typed in the console, and all of the output that streams by in the console.
Download data we’ll use in class. Create a new folder somewhere on your computer that’s easy to get to (e.g., your Desktop). Name it bioconnector. Inside that folder, make a folder called data, all lowercase. Download the data files below, saving them to the new bioconnector/data folder you just made.
Recommended reading: This lesson does not cover methods and software for generating phylogenetic trees, nor does it it cover interpreting phylogenies. Here’s a quick primer on how to read a phylogeny that you should review prior to this lesson, but it is by no means extensive. Genome-wide sequencing allows for examination of the entire genome, and from this, many methods and software tools exist for comparative genomics using SNP- and gene-based phylogenetic analysis, either from unassembled sequencing reads, draft assemblies/contigs, or complete genome sequences. These methods are beyond the scope of this lesson.
R version 3.4.0 was released April 2017. If you have not updated your R installation since then, you need to upgrade to a more recent version, since several of the required packages depend on a version at least this recent. You can check your R version with the sessionInfo() command.↩︎
Installing/loading the tidyverse tidyverse will install/load the core tidyverse packages that you are likely to use in almost every analysis: ggplot2 (for data visualisation), dplyr (for data manipulation), tidyr (for data tidying), readr (for data import), purrr (for functional programming), and tibble (for tibbles, a modern re-imagining of data frames). It also installs a selection of other tidyverse packages that you’re likely to use frequently, but probably not in every analysis (these are installed, but you’ll have to load them separately with library(packageName)). This includes: hms (for times), stringr (for strings), lubridate (for date/times), forcats (for factors), DBI (for databases), haven (for SPSS, SAS and Stata files), httr (for web apis), jsonlite (or JSON), readxl (for .xls and .xlsx files), rvest (for web scraping), xml2 (for XML), modelr (for modelling within a pipeline), and broom (for turning models into tidy data). After installing tidyverse with install.packages("tidyverse") and loading it with library(tidyverse), you can use tidyverse_update() to update all the tidyverse packages installed on your system at once.↩︎
We’ll talk about this in class. It’s not a concern.↩︎
This means the version of R you have installed is older than the version that the package author used when they built the package you’re trying to use. 99% of the time it isn’t a problem, unless your R version is very old (you should be using 3.4.0 or later for this course).↩︎