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
3. Set this up on your own computer
- If you're using Windows, install git
- 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
- Clone this repository and all submodules
git clone --recursive https://github.com/YeoLab/single-cell-bioinformatics
- Go to the new directory
- Create a new environment with the necessary packages
conda create --yes -n single-cell-bioinformatics --file conda_requirements.txt
- Activate the environment
source activate single-cell-bioinformatics # On windows, do "activate single-cell-bioinformatics"
- Install the remaiing requirements
pip install -r requirements.txt
- PHEW. Now you can launch the notebooks!!