diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..60b39950759149de1cfe97f1f9321053d36f2824 --- /dev/null +++ b/README.md @@ -0,0 +1,27 @@ +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. +