Metadata-Version: 2.1
Name: berets
Version: 0.1.2
Summary: Tools for analyzing CRISPR data with REPorter edits
Home-page: https://github.com/pinellolab/beret
Author: Jayoung Ryu
Author-email: jayoung_ryu@g.harvard.edu
License: UNKNOWN
Description: # <img src="beret.svg" alt="beret" width="300"/>
        **B**ase **E**diting with **Re**porter analysis **T**oolkit.  
        This is an analysis toolkit for the pooled CRISPR reporter or sensor data. The reporter technique transfects cells with plasmid with not only sgRNA but with the **target sequence surrogate** which we call **reporter** or **sensor**.  
          
        <img src="anbe.svg" alt="anbe" width="500"/>
        
        ## Installation 
        Downloading from PyPI:
        ```
        pip install berets
        ```
        
        ## Count reporter screen data  
        Aligns guide with matched reporter allele counts in multiple samples.  
        
        <img src="reporter_screen.svg" alt="reporter screen" width="700"/>  
        
        ```python
        beret-count-samples         \
          --input sample_list.csv   \ # sample with lines 'R1_filepath,R2_filepath,sample_name\n'  
          -b A                      \ # base that is being edited (A/G)
          -f gRNA_library.csv       \ # sgRNA information 
          -o .                      \ # output directory    
          -a                        \ # read allele information  
          -r                        \ # read reporter edit information
          -m                        \ # read matched guide and reporter edit information  
          -t 12                     \ # number of threads  
          --name LDLvar_fullsort    \ # name of this sample run  
        ```
        
        This produces `.h5ad` and `.xlsx` file with guide and per-guide allele counts.  
        `.h5ad` file follows annotated matrix format compatible with `AnnData` and is based on `Screen` object in [purturb_tools](https://github.com/pinellolab/perturb-tools) and contains the per-guide allele counts.    
        <img src="screendata.svg" alt="screendata" width="700"/>
        
        ## Using as python module
        ```
        import beret as br
        cdata = br.read_h5ad("beret_counts_sample.h5ad")
        ```
        
        See the [tutorial](beret_test.rst) for more detail.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
