Course material in notebook format for learning about single cell bioinformatics methods. To view this material, you have several options:

Where you can run and edit code (also accessible by clicking the pink "launch binder" badge above)

Where you cannot run or edit code, but view all the content

• 0. If you're using Windows, install git
• 1. Install Miniconda with Python 3. Command line instructions for mac and linux are shown below.

# Mac OS X
curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > miniconda.sh

# 64-bit Linux
curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh

# After downloading, install (both Mac and Linux)
bash -b miniconda.sh

• 2. Clone this repository and all submodules

git clone --recursive https://github.com/YeoLab/single-cell-bioinformatics

• 3. Go to the new directory

cd single-cell-bioinformatics

• 4. Create a new environment with the necessary packages

conda create --yes -n single-cell-bioinformatics --file conda_requirements.txt

• 5. Activate the environment

source activate single-cell-bioinformatics  # On windows, do "activate single-cell-bioinformatics"

• 6. Install the remaiing requirements

pip install -r requirements.txt

• 7. PHEW. Now you can launch the notebooks!!

jupyter notebook

• SCRM 2016