Setup your system

1. Install conda
2. Add relative channels

# add channels 
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels r
conda config --add channels python

3. Create fresh environment for your task and install packages locally.

Exploratory data analysis

How to use Jupyter with multiple conda environments? Install nb_conda_kernels in the base environment or separate environment you used for jupyter stuff.

conda install -c conda-forge nb_conda_kernels

Using nb_conda_kernels, you can have one Jupyter installed in your system and launch different python or R kernels form any created conda environments even in a single notebook.

Note: You only need ipykernel, numpy and pandas in each environment in addition to your own packages.

conda install -n <env-name> -c anaconda ipykernel numpy pandas

How to use R (and python) in Jupyter? Instead, you can include R kernel into an envrinment with R packages. So, install irkernel. How to tunnel from your local machine to the server? I could almost always use this: ssh -NfL 1111:localhost:2222 @.ucsf.edu Replace 2222 with Jupyter port number in the server and 1111 with your desired local port number.

Tutorials

Part 1: Alignment

Tutorial notes

Part 2: Differential expression analysis

Tutorial notes