Analysis resources for the publication Pooled genetic perturbation screens with image-based phenotypes. This is an updated and expanded version of the repository for the original 2019 publication Optical pooled screens in human cells, available here.
Download the repository (e.g., on Github use the green "Clone or download" button, then "Download ZIP").
In Terminal, go to the OpticalPooledScreens2023 project directory and create a conda environment using a command like:
conda create --name sbs_2023 python=3.8
This creates a conda environment called sbs_2023
for project-specific resources.
conda activate sbs_2023
pip install wheel
pip install -r requirements.txt
pip install -e .
Additionally, if running CellPose segmentation locally and you want to use the gui:
python -m pip install cellpose[gui]
To run the analysis pipeline with images from the original publication, first download and install the IBM Aspera Command Line Interface (includes ascp
) for interaction with the Cell-IDR databse. Then, set up an example directory:
python -m ops.paper.cell_idr setup_example example --ascp=<path/to/ascp/executable>
Note that if ascp
is in your path, you can use --ascp==ascp
.
Run the pipeline on the example data using snakemake (after activating the virtual environment):
cd example
snakemake --cores all --configfile=config.yaml
An example tile of 12-cycle SBS data is available in the original OpticalPooledScreens repository here.
Additionally, all screening data presented in the original publication can be easily accessed from the public Cell-IDR database (study idr0071
) using ascp
similar to above for the example pipeline:
python -m ops.paper.cell_idr get_cell_idr \
<destination> \
--experiment=<experiment> \
--well=<well> \
--tile=<tile> \
--ascp=<path/to/ascp/executable>
The following experiments are available:
Cell-IDR experiment | Dataset |
---|---|
A | static p65-mNeonGreen screen in HeLa cells |
B | static p65 antibody screen in HeLa cells |
C | static p65 antibody screen in A549 cells |
D | static p65 antibody screen in HCT-116 cells |
E | Frameshift reporter screen in HeLa cells |
F | Detection of combinatorial perturbations in HeLa cells |
Both well
and tile
can be set to all
to download the full dataset. Figures 3 & 4 in the Nature Protocols manuscript were made using data from experiment C; functions for reproducing these figures are available here.