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add a figure for common types of screens
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abearab authored Dec 8, 2023
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Expand Up @@ -13,8 +13,11 @@ Genomics evolves and newer CRISPR screen platforms are developed.
For more information about the statistical methods used in ScreenPro2, please refer to the detailed documentation
about [PhenoScore](https://screenpro2.readthedocs.io/en/latest/PhenoScore.html) module.

Note that ScreenPro2 starts with a counts matrix of oligo counts (samples x oligos) so you will need to process your
raw sequencing data into a counts matrix before using ScreenPro2.
> From: [A new era in functional genomics screens](https://www.nature.com/articles/s41576-021-00409-w)
> Fig. 1: Common types of CRISPR screening modalities indicating advances in CRISPR methods.
> <img width="1000" alt="image" src="https://github.com/GilbertLabUCSF/ScreenPro2/assets/53412130/a39400ad-b24f-4859-b6e7-b4d5f269119c">
## Installation
ScreenPro2 is available on PyPI and can be installed with pip:
Expand All @@ -28,6 +31,8 @@ pip install git+https://github.com/abearab/ScreenPro2.git
```

## Usage
Note that ScreenPro2 starts with a counts matrix of oligo counts (samples x oligos) so you will need to process your
raw sequencing data into a counts matrix before using ScreenPro2.

### Load Data
First, load your data into an `AnnData` object (see [anndata](https://anndata.readthedocs.io/en/latest/index.html) for
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