From 08735c9550796ebe6ea9507a9856d7b9a08d8473 Mon Sep 17 00:00:00 2001 From: abearab Date: Fri, 8 Dec 2023 16:16:34 -0800 Subject: [PATCH] change #24 --- README.md | 30 ++++++++++++++++++++++-------- 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index e195c34..7440d81 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,28 @@ ![image](https://img.shields.io/pypi/v/screenpro2.svg) [![Documentation Status](https://readthedocs.org/projects/screenpro2/badge/?version=latest)](https://screenpro2.readthedocs.io/en/latest/?version=latest) ![Downloads](https://static.pepy.tech/badge/screenpro2) -ScreenPro2 -========== +# ScreenPro2 - +The complete docs are available at [screenpro2.rtfd.io](https://screenpro2.readthedocs.io). + +## Table of Contents +- [Installation](#installation) +- [Usage](#usage) + * [Load Data](#load-data) + * [Perform Screen Processing Analysis](#perform-screen-processing-analysis) + + [Drug Screen Workflow: calculate `gamma`, `rho`, and `tau` scores](#drug-screen-workflow-calculate--gamma----rho----and--tau---scores) + + [Flow cytometry based screen workflow: calculate phenotype score to compare high and low bins](#flow-cytometry-based-screen-workflow-calculate-phenotype-score-to-compare-high-and-low-bins) +- [Supported CRISPR Screen Platforms](#supported-crispr-screen-platforms) + + [CRISPRi-dual-sgRNA-screens](#crispri-dual-sgrna-screens) +- [License](#license) +- [Citation](#citation) + +## Introduction This package is conceptually similar to the [**ScreenProcessing**](https://github.com/mhorlbeck/ScreenProcessing) pipeline but **ScreenPro2** is designed to be more modular, flexible, and extensible as the field of Functional -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. +Genomics evolves and newer CRISPR screen platforms are developed. Common CRISPR screen methods that we have +implemented here are illustrated in a recent review paper: > From: [A new era in functional genomics screens](https://www.nature.com/articles/s41576-021-00409-w) @@ -108,7 +119,7 @@ Currently, ScreenPro2 has easy-to-use workflows for the following CRISPR screen #### CRISPRi-dual-sgRNA-screens [Replogle et al., _eLife_ (2022)](https://elifesciences.org/articles/81856) -Replogle et al. developed a CRISPRi screening platform that uses two sgRNAs per gene within a single plasmid and it has +Replogle et al. developed a CRISPRi screening platform that uses two sgRNAs per gene within a single plasmid, and it has been used to perform genome-scale CRISPRi screens. If you follow the codes in the provided [GitHub repository](https://github.com/josephreplogle/CRISPRi-dual-sgRNA-screens), you will end up with oligo counts and once you make `ScreenPro` object, you can use the ScreenPro2 workflow for this platform to calculate the enrichment of each gene between screen arms. @@ -116,3 +127,6 @@ platform to calculate the enrichment of each gene between screen arms. ## License ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE) for more information) and developed by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)), a Research Associate in the Gilbert lab at UCSF and Arc Institute. + +## Citation +If you use ScreenPro2 in your research, please cite the following paper. \ No newline at end of file