https://github.com/YeoLab/single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods
https://github.com/YeoLab/single-cell-bioinformatics

Last synced: 23 days ago
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Course material in notebook format for learning about single cell bioinformatics methods

• Host: GitHub
• URL: https://github.com/YeoLab/single-cell-bioinformatics
• Owner: YeoLab
• License: bsd-3-clause
• Archived: true
• Created: 2016-05-04T15:05:43.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2016-06-19T01:06:45.000Z (about 8 years ago)
• Last Synced: 2024-05-22T18:13:09.017Z (about 1 month ago)
• Language: Jupyter Notebook
• Size: 39.9 MB
• Stars: 97
• Watchers: 16
• Forks: 37
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome_single_cell - CSHL Single Cell Analysis - Bioinformatics - Uses Shalek 2013 and Macaulay 2016 datasets to teach machine learning to biologists (Tutorials and workflows / Other applications)

README

        
[![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/YeoLab/single-cell-bioinformatics)

# single-cell-bioinformatics

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

## 1. View the [live version](http://mybinder.org/repo/YeoLab/single-cell-bioinformatics) 

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

## 2. View the [static version](http://nbviewer.jupyter.org/github/yeolab/single-cell-bioinformatics/blob/master/index.ipynb) 

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

## 3. Set this up on your own computer

* 0. If you're using Windows, install [git](https://msysgit.github.io/)

* 1. Install [Miniconda](http://conda.pydata.org/miniconda.html) 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

```

## Frozen versions of previous implementations

* [SCRM 2016](https://github.com/YeoLab/single-cell-bioinformatics-scrm-2016)