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KrishnaswamyLab / scprep

A collection of scripts and tools for loading, processing, and handling single cell data.
MIT License
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Feature/dyngen #119

Closed aarthivenkat closed 3 years ago

aarthivenkat commented 3 years ago

Dyngen is a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. The backbone of a dyngen model determines the overall dynamic process that a cell will undergo during a simulation. It consists of a set of gene modules, which regulate each other in such a way that expression of certain genes change over time in a specific manner.

dyngen.py consists of three functions to (1) install dyngen (2) get a list of backbones, and (3) generate simulated datasets. Generating simulated datasets by default will return a cell_info dataframe and an expression dataframe. Optional arguments offer ground truth regulatory networks (bulk and cellwise) and RNA velocity measurements.

More information at https://github.com/dynverse/dyngen.

scottgigante commented 3 years ago

One more note - these formatting issues should be fixed: https://github.com/aarthivenkat/scprep/runs/1936473492?check_suite_focus=true#step:7:1

coveralls commented 3 years ago

Coverage Status

Coverage decreased (-0.07%) to 97.899% when pulling 168cff9d2f54afb6a4e1c71f154891379ad47354 on aarthivenkat:feature/dyngen into b0566ce40e6bac5694dcde0ddd929716d449e87d on KrishnaswamyLab:dev.

scottgigante commented 3 years ago

Also, could you please write tests for lib and dependencies?

scottgigante commented 3 years ago

Thanks for the PR!