MDhewei / protiler

ProTiler method for the analysis and visualization of CRISPR screens with tiling-sgRNA design
https://github.com/MDhewei/ProTiler-1.0.0
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crispr-analysis protein-domain-identification tiling-sgrna-screen

License: GUN

Introduction of ProTiler

ProTiler is a novel computational method for fine-mapping of protein regions that are 
hyper-sensitive to CRISPR/Cas9 mediated gene knockouts(CKHS region) from high-throughput 
tiling-sgRNA functional screens. 

Also, ProTiler is able to predict CKHS regions for protein encoded by any given gene from 
other common protein features including conservation, domain annotation, secondary structures 
and PTMs distribution.

If you use ProTiler please cite the following paper we published on Nature Communications:

He et al. De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA 
knockout screens. Nat Commun 10, 4547(2019).

Recent Changes for ProTiler

1) New version 1.0.2 is now compatible to python3.

2) The package has been uploaded to PyPI. Users now can install directly through:

   pip install protiler

Installation

ProTiler is written in Python and R, Python>=2.7 and R>=3.5.0 is needed

Note: Since some large files are uploaded using git lfs, make sure git lfs is installed before downloading

Dependencies

Python Packages:

  • scikit-learn==0.22.1, matplotlib >=2.2.3, pandas >=1.2.0, numpy >=1.17.5, seaborn >=0.9.0

R packages:

  • breakfast(v0.1.0), stringr

Step1: Install Anaconda (highly recomended)

wget https://repo.continuum.io/archive/Anaconda2-2018.12-Linux-x86_64.sh 
bash Anaconda2-2018.12-Linux-x86_64.sh 

Step2: Install required packages

Install Python Packages with pip:

pip install matplotlib pandas sklearn numpy seaborn

Install R packages in R IDE:


install.packages('stringr')

require(devtools) install_version("breakfast", version = "0.1.0", repos = "http://cran.us.r-project.org")


### Step3: Install ProTiler 
#### Note: Since some large files are uploaded using git lfs, make sure git lfs is installed before downloading

```console
git clone https://github.com/MDhewei/ProTiler-1.0.0.git
cd ProTiler-1.0.0
python setup.py install

Usage

ProTiler has two major functions:

1. Call: Call and visualize HS regions from CRISPR tiling screen data.

Protiler call take table file(.cvs or .txt) recording CRISPR tiling screen data as input.An example is shown as below:

Three colums are required:

Arguments of the program:

Required arguments:

Optional arguments:

Example to run protiler call

protiler call -i sample.txt -g CREBBP -s 9,10,11 -o ProtilerOutput

Output

1. SegmentFile: A table record all the HS regions called by ProTiler for certain gene.

2. Figure4Visualization: Figure presenting signals, HS regions and other protein annotations. For example:

2. Predict: Predict and visualize HS regions from common protein features.

Arguments of the program:

Required arguments:

Optional arguments:

Example to run protiler predict

protiler predict -l CREBBP,FAM122A,SAMRCB1,AURKB -o ProtilerOutput

Output

1. PredictionTable: A table record all the features of target protein and SVM score/class at each residue postion.

2. Figure4Visualization: Figure presenting predicted HS regions and other protein annotations. For example: