conda_env_instructions_for_mac.md

1. Install miniconda or anaconda with python version 3.6 or above.

2. Run the following commands for conda and pip

conda update --all
conda install r-essentials r-rgl
conda install pandas numpy scipy scikit-learn jupyter gsl tzlocal simplegeneric natsort h5py tqdm patsy llvmlite numba networkx joblib numexpr pytables seaborn statsmodels pip
conda install -c conda-forge python-igraph louvain

pip install --upgrade pip
pip install MulticoreTSNE anndata anndata2ri fa2 gprofiler-official scanpy rpy2

MulticoreTSNE is optional and just for speed, so leave it out if you run into problems installing it.

3. Start R and run the following commands:

install.packages(c('devtools', 'gam', 'RColorBrewer', 'BiocManager'))
update.packages(ask=F)
BiocManager::install(c("scran","MAST","monocle","ComplexHeatmap","slingshot"), version = "3.8")