louisfaure / adrenal5htp_paper

Adrenal5HTP

Raw and processed data is available on the following GEO Series: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180861

Environment setup

conda create -n 5HTP -c anaconda python=3.9 -y
conda activate 5HTP
pip install brie==2.0.5 scanpy scFates

GPU (Optional)

BRIE code can be accelerated with CUDA GPU.

conda install -c anaconda cudatoolkit -y
pip install -U tensorflow-gpu

Running the notebooks

1. Process.ipynb scRNAseq data pre-processing, clustering and embedding generation.
2. BRIE2.ipynb running BRIE2 pipeline, requires BAM files generated from alignment.
3. Plots.ipynb to generate plots for the manuscript.