A GenePattern Module to view NGCHM in GenePattern Notebook.Detail document.
- After login, click on the dropdown list to insert a GenePattern Cell.
- Select Next.Gen.Cluster.Heat.Map.Viewer module.
- Upload a ngchm file or paste URL to a ngchm file. Sample NGCHM File
- Download GenePattern, double click to install on local machine.
- Input Email, the app will ask to restart, double click on icon again.There is no need to install other modules if you only want to try NGCHM builder and viewer.
- Type "ant" to build zip file for the module.
- Click on "Modules & Piplelines", then click on "Install from zip".
- Chose to upload Next.Gen.Cluster.Heat.Map.Viewer.zip file in the build folder.
- Jupyter notebook is installed in Anaconda.
- Install GenePattern notebook using pip.
pip install genepattern-notebook
- Enable extenstion.
jupyter nbextension enable --py widgetsnbextension
jupyter nbextension install --py genepattern
jupyter nbextension enable --py genepattern
jupyter serverextension enable --py genepattern
jupyter nbextension install --py nbtools
jupyter nbextension enable --py nbtools
jupyter serverextension enable --py nbtools
- Launch Jupyter.
jupyter notebook
Guide from GenePattern Notebook site.
- Install genepattern notebook from dockerhub.
docker pull genepattern/genepattern-notebook
- Run genepattern notebook docker.
docker run -p 8889:8888 -name genepattern-notebook genepattern/genepattern-notebook
- Copy the URL shown on the screen, paste into browser, change port number to 8889.