HeLa DMEM and HPLM whole genome datasets

Note that this repository contains the configuration used to generate the profiles and QC information generated by the recipe and does not contain all of the recipe outputs. Download instructions for the single cell data and profiles generated through this recipe can be found in the corresponding publication repository.

Pooled Cell Painting: Data Pipeline Welding Template 🛠️

This repository was derived from a template repository located at https://github.com/broadinstitute/pooled-cell-painting-profiling-template. The purpose of the repository is to weld together a versioned data processing pipeline with versioned processed output data for a single Pooled Cell Painting experiment.

Figure 1: Data Pipeline Welding is a procedure that links together version controlled data with a version controlled processing pipeline. The procedure results in a new repository for each dataset within a Pooled Cell Painting project. The pooled-cell-painting-profiling-recipe repository contains the data processing pipeline. The pooled-cell-painting-profiling-template (this repo) contains recipe configuration files that must be edited for each dataset. A user's recipe fork is added to the dataset-specific repo as a Github submodule. The weld is finalized when the user prepares the recipe, outputting version controlled morphology profiles that are used for downstream biological discovery.

Notes about terminology:

• A batch is the data pipeline welding unit, and a batch consists of one or more plates.
• A batch can also be referred to as a dataset.
• An experiment is designed around a specific question and may contain single or multiple batches, depending on the experimental design.
• A project is an encompassing term and may contain any number of experiments (and therefore any number of batches).