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Here is our schedule of activities:
To follow along on the practice examples, you will need to install R and R studio. R is a programming environment and R Studio is a GUI (graphic user interface) to make working with R easier. R is available from CRAN. Download the version for your operating system (pc or mac) and double-click the downloaded program to install it on your local computer. After R is installed you can download RStudio here. Again, pick the version for your operating system, download the installer, and open the installer to put RStudio on your local computer.
Once you have R and R studio installed, you will need to install several packages for R.
First, you will need to install devtools. Using the tools tab in RStudio, open the "Install packages" option. When the new window opens, make sure "Install dependencies" is checked (this will install additional packages required to run the specific package being installed). Type "devtools" into the "Package" blank and click "Install."
Next you will need to install BiocManager (aka Bioconductor) from the RStudio tools tab. Type "BiocManager" into the "Package" blank and click "Install." Check the box to install dependencies.
Once you have devtools and bioconductor installed, you will need to install programs from the R studio console window using the following commands.
library(devtools)
devtools::install_github('ggloor/CoDaSeq/CoDaSeq')
After updating my version of R and RStudio, I had to re-install all these packages. When I tried to reinstall codaseq, I got the following error in Rstudio:
Using GitHub PAT from the git credential store. Error: Failed to install 'unknown package' from GitHub: HTTP error 401. Bad credentials Rate limit remaining: 55/60 Rate limit reset at: 2024-05-17 14:29:06 UTC
I had to go to my Github account in the website to generate a Personal Access Token (PAT). You do this from the settings, as described here for "creating a personal access token (classic)". Copy the new PAT and then insert it between the quotation marks in the following command for the Rstudio console:
Sys.setenv(GITHUB_PAT = "your-new-PAT")
Then simply retry the installation:
devtools::install_github('ggloor/CoDaSeq/CoDaSeq')
library(BiocManager)
BiocManager::install("dada2")
BiocManager::install("ShortRead")
BiocManager::install("phyloseq")
From the RStudio Tools tab, also install the following libraries:
- ggplot2
- vegan
Depending on how much time we have left, we will talk about Rmarkdown versus R scripts, setting up working directory, and introduction to Github desktop.
One drive folder with sequence dataLinks to an external site.
Sequence data can be downloaded to your local computer in two ways. If you are experienced with Github Desktop, you can clone the repository locally to your own computer. Most of you will not be familiar with Github Desktop and can therefore most easily downloaded the sequence data from this one drive directory. Download the "cutadapt" directory to your local computer. Uncompress the "cutadapt" directory locally after downloading, but do not uncompress the fastq.gz files.