jubilant-barnacle

Getting Data

use gdown https://drive.google.com/drive/folders/1XiVwOaTIxERE5Kf2T2lAfuW8sLL3IS8u?usp=sharing to download files from paper

Analysis Notebooks

Analysis ipynbs show results from CSHMM training for various different runs

• scRNA-seq data only: (cv = cross validation, kc6 = starting with 6 initial clusters in scdiff, split6 = 6 initial splits during CSHMM training
• scRNA-seq/scATAC-seq: (integrated)

Other Notebooks and scripts

• monocle3_analysis.R: processing steps for analyzing data with monocle
• format_data.ipynb: formatting raw data & renaming clusters into pseudotime
• get_paper_cluster_markers.ipynb: getting top (by p-value) markers for each cluster
• run_cshmm.ipynb: testing running CSHMM training (before moving to doing training on the cluster)
• output_analysis.ipynb: exploratory data analysis for CSHMM training outputs

Setup:

conda_envs folder

• conda_envs/env_setup.ipynb: instructions for installing dependencies for cshmm & scdiff2 (must be done in separate conda envs because they use different versions of python)
• final_cshmm_env.yml: conda env spec for running cshmm
• scdiff2_env: conda env spec for running scdiff2

data processing

• format_data.ipynb: processing raw scRNA-seq data for CSHMM and scdiff
• formated_integrated_data.ipynb: processing integrated scRNA-seq/scATAC-seq for CSHMM and scdiff