Name: multi-omic-urothelial-anti-pdl1
Owner: Hammer Lab
Description: Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis
Created: 2016-10-20 00:26:16.0
Updated: 2017-05-11 22:21:02.0
Pushed: 2017-10-31 22:34:07.0
Size: 331807
Language: Jupyter Notebook
GitHub Committers
User | Most Recent Commit | # Commits |
---|
Other Committers
User | Most Recent Commit | # Commits |
---|
In the interest of full transparency, please note that calculated numbers and figures are directly linked to their source Jupyter notebooks in this repository throughout our preprint.
To get started, install the requirements:
install -r requirements.txt
Create an ENV.sh
modeled after ENV_TEMPLATE.sh
, pointing to the data that you have available, and then call run.sh
to source
your ENV.sh
in the context of a new Jupyter notebook.
Certain notebooks in this repo require rpy2
. rpy2
will be installed via the requirements.txt
, but depending on your environment may require additional setup.
In order to execute the notebooks, you will need to have:
Specifically:
stall R, if you haven't already
apt-get install r-base r-base-dev
eate & set personal rlib directory, if not already done
siest way to do this is to open an interactive R console, and run
tions(repos = 'https://cran.rstudio.com')
stall.packages('ggplot2')
nstall certain R packages
"options(repos = 'https://cran.rstudio.com'); install.packages(c('dplyr','survival','tidyr','ggplot2'));"