Quick start

System requirements:

Linux/Unix Python (>= 3.7)

Install Scanpy through conda:

The Miniconda3 package management system can be used to harmonize all of the software packages. We can install Scanpy using the conda environment. Use the following commands to install Minicoda3£º $ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh $ bash Miniconda3-latest-Linux-x86_64.sh

##We can create an isolated environment for Scanpy and install through the following commands: $ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge $ conda create -n scanpy_env python=3.7 $ conda activate scanpy_env $ conda install seaborn scikit-learn statsmodels numba pytables $ conda install -c conda-forge python-igraph leidenalg $ conda install -c bioconda scanpy $ conda install -c anaconda ipykernel

Clone the repository:

$ git clone git@gitlab.rc.uab.edu:attis2021/single_cell_rnaseq_scanpy.git

Tutorial:

A more detailed tutorial of how to analyze PBMC data use Scanpy can be found in file scanpy_pbmc_tutorial.ipynb.