project_template

A template repository for pipeline code. For an example, see https://github.com/IGVF-UCSD/celloracle_pipeline/tree/dev. This should include:

README.md

• with details of the project
• mention where you can find pipelines and datasets

dataset_1

• README.md with brief details on dataset and pointer to how it was processed

bin

• Compiled code (scripts and notebooks) for downstream analysis relevant to this project
• Will usually be some combination of bash scripts for running pipelines and notebooks for visualizing results

figures

• Figures generated from notebooks

results

• Outputs from running pipelines

dataset_2

• …

doc

• Any text or links to spreadsheet, docs etc.

auxiliary_data

• Links or data that is used for analysis but not explicitly generated here