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Tutorials & Case Studies

Hands-on ways to build skills with CRN Cloud data and see those skills applied to real research questions.

If you have not yet set up data access and a Verily Workbench workspace, start with Requesting Data Access and the Verily Workbench Guide first.

Tutorials

Tutorials are hands-on modules for building core skills with CRN Cloud data. Each tutorial series includes an environment.yml to help recreate the required software environment.

Pilot Workshop Series

Sequential, numbered notebooks that provide a guided path from first connection to a basic analysis.

Located in:

text tutorials/Workshops/00_pilot_workshop_series/

Notebook What it teaches
01_getting_started.ipynb Connect to CRN Cloud and load your first dataset
02_data_exploration.ipynb Explore metadata, visualize distributions, and inspect quality
03_downstream_analysis.ipynb Run differential expression and basic statistical analyses

Best for: first-time users who want a guided, sequential introduction.

Sample Notebooks

Standalone references, not a sequence. These are useful once you already know what you are looking for or want a quick example in Python or R.

Located in:

text tutorials/Sample_Notebooks/

Notebook What it teaches
Py3_Explore_ASAP_CRN_Data.ipynb Introduction to working with CRN data on Verily Workbench using Python
R_Explore_ASAP_CRN_Data.ipynb Introduction to working with CRN data on Verily Workbench using R

Best for: users who want a quick reference rather than a guided sequence.

Case Studies

Case studies apply pipeline outputs and Workbench tools to a specific biological question, end to end.

Unlike the tutorials above, case studies live in their own top-level case_studies/ folder in the repository. Each case study includes its own environment.yml and README.md with background and setup instructions.

Substantia Nigra Cell-Type Annotation

Located in:

text case_studies/SN_CellType_Annotation/

Notebook Step
sn_celltyping__part01_setup.ipynb Setup
sn_celltyping__part02_preprocessing.ipynb Preprocessing
sn_celltyping__part03_mapmycells.ipynb MapMyCells annotation

Best for: seeing how data access, Verily Workbench, and the scRNA-seq pipeline cell-type annotation strategy come together in an applied research workflow.

Prerequisites

Before running any tutorial or case study, make sure you have:

Each tutorial or case study folder includes its own environment.yml. Install the appropriate environment before running the notebooks.