ISMB.mutsig.tutorial

Welcome to the ISMB2020 Online Mutational Signature Analysis Tutorial, July 11 and 12, 2020 (https://www.iscb.org/ismb2020-program/tutorials#tut1)

Signature extraction excercise is at

https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/exercise.in.interpreting.extraction.results.zip

The input data was not in the .zip; it is at

https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/3.types.ground.truth.spectra.1000.size.csv

(1000.size refers to a dispersion parameters I used when adding variance to the spectra.)

Slack info

To register for slack account: https://join.slack.com/t/international-pll7528/shared_invite/zt-fjw1i0g5-ogelj7jCcV8fYEy7afwfgg
After you signed up for an account, join the session for this tutorial: https://international-pll7528.slack.com/archives/C01763XTWPJ

Please do before the tutorial

1.Please have R >= 4.0.0 installed on your computer. You can find the latest release at https://cloud.r-project.org/

2.Please install the package ICAMS and its prerequisites from CRAN.

install.packages("ICAMS")

3.Please install BSgenome.Hsapiens.1000genomes.hs37d5 from Bioconductor:

install.packages("BiocManager")
BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")

4.Additional R libraries that will be needed:

4.1 CRAN packages: philentropy, gplots, factoextra

install.packages("philentropy")
install.packages("gplots")
install.packages("factoextra")

4.2 GitHub packages:

Thare are 2 ways to install these.

4.2.1 If you do not have Rtools (Windows) or XCode (Mac), then download from

https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/PCAWG7_0.0.1.tar.gz

https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/mSigBG_1.0.0.tar.gz

and put them in the current working directory for your R session, and then

install.packages("PCAWG7_0.0.1.tar.gz", repos = NULL, type = "source")
install.packages("mSigBG_1.0.0.tar.gz", repos = NULL, type = "source")

We think you will get a warning, but we think the installations will work.

4.2.2

If you have Rtools (Windows) or XCode (Mac), you can install the GitHub packages with the R command line:

install.packages("remotes")
remotes::install_github("steverozen/mSigBG", ref = "1.0-branch", force = TRUE)
remotes::install_github("steverozen/PCAWG7", force = TRUE)

If you want to install Rtools (Windows) or XCode (Mac), the instructions are as follows:

Windows:
Please download and install Rtools from CRAN: https://cran.rstudio.com/bin/windows/Rtools/.

macOS:
Please install the Command Line Tools for XCode. You can do this in one of two ways.

Either:

1. Download and install XCode from the Mac AppStore: http://itunes.apple.com/us/app/xcode/id497799835?mt=12

2. Within XCode go to Preferences : Downloads and install the Command Line Tools

Or alternatively (for a smaller download size):

1. Register as an Apple Developer (free) here: https://developer.apple.com/programs/register/

2. Download the Command Line Tools for XCode appropriate for the version of macOS you are running from here: https://developer.apple.com/downloads/

Linux:
For Debian/Ubuntu, you can install the development utilities required by executing:

sudo apt-get install r-base-dev

For other versions of Linux please consult their documentation to determine how to install a basic GNU development tool chain.

If you have difficulties contact Nanhai JIANG at nanhai.jiang@u.duke.nus.edu.

You will need R and the above packages for the practicum on July 11.

The practicum inputs

The inputs are at https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/ISMB.mutational.sigatures.practicum.zip.

The slides

0. https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.Lecture.0.short.intro.pptx
1. https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.Lecture.1.Mutational-Signatures%202020_07_10.pptx
2. https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.Lecture.2.data-mining.NMF.and.HPD.2020.07.10.pptx
3. https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.lecture.3.landscape_tactics_20200710.pptx