Bioinformatics of Genomic Medicine 2018
Install these tools before the workshop:
1) A robust text editor.
- For Windows/PC - notepad++
- For Linux - gEdit
- For Mac – TextWrangler
2) A file decompression tool.
3) A robust internet browser such as Firefox or Safari (Internet Explorer and Chrome are not recommended because of Java issues).
4) SSH client - Mac and Linux users already have a command line ssh program that can be run from the terminal. For Windows users, please download PuTTY.
5) SCP/SFTP client - We will be moving data from the servers to the student laptops for visualization. Mac and Linux users already have a command line scp and sftp program. For Windows users, please install WinSCP.
6) A PDF viewer (Adobe Acrobat or equivalent).
7) Latest version of R and RStudio. If asked to also install git, select yes.
8) Install the BioConductor core packages. To do this, open RStudio and type the following at the > prompt:
source("http://bioconductor.org/biocLite.R");
biocLite();
9) Install some workshop specific packages in RStudio. At the > prompt, type:
install.packages("SNFtool");
install.packages("gplots");
install.packages("RColorBrewer");
install.packages("glmnet");
install.packages("ggplot2");
install.packages("reshape2");
install.packages("pROC");
install.packages("caret");
install.packages("matrixStats");
source("http://bioconductor.org/biocLite.R");
biocLite("minfi");
biocLite("bumphunter");
biocLite("limma");
biocLite("lumi");
biocLite("sva");
11) sqlitebrowser
Read these papers before the workshop:
The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease
PhenoTips: patient phenotyping software for clinical and research use
IHEC Data portal
Do these tutorials before the workshop:
1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.
- The CBW R tutorial
- Quick and Dirty Guide to R
- The R Tutorial up to and including 5. Basic Plots
- The R command cheat sheet
2) UNIX Preparation tutorials:
Please note that these instructions may change prior to the workshop.