Welcome to the ISMB2020 Online Mutational Signature Analysis Tutorial, July 11 and 12, 2020 (https://www.iscb.org/ismb2020-program/tutorials#tut1)
The input data was not in the .zip; it is at
(1000.size refers to a dispersion parameters I used when adding variance to the spectra.)
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
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:
-
Download and install XCode from the Mac AppStore: http://itunes.apple.com/us/app/xcode/id497799835?mt=12
-
Within XCode go to Preferences : Downloads and install the Command Line Tools
Or alternatively (for a smaller download size):
-
Register as an Apple Developer (free) here: https://developer.apple.com/programs/register/
-
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 inputs are at https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/ISMB.mutational.sigatures.practicum.zip.
- https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.Lecture.0.short.intro.pptx
- https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.Lecture.1.Mutational-Signatures%202020_07_10.pptx
- https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.Lecture.2.data-mining.NMF.and.HPD.2020.07.10.pptx
- https://github.com/steverozen/ISMB.mutsig.tutorial/raw/master/Tut1.lecture.3.landscape_tactics_20200710.pptx