Metadata-Version: 2.1
Name: luciferase
Version: 1.5.2
Summary: Helper functions for luciferase data
Home-page: https://github.com/anthony-aylward/luciferase.git
Author: Anthony Aylward, Joshua Chiou, Mei-Lin Okino
Author-email: aaylward@eng.ucsd.edu
License: UNKNOWN
Description: # luciferase
        Tool for plotting luciferase reporter data. Thanks due to Joshua Chiou and Mei-lin Okino for inspiration and contributions.
        
        ## Installation
        ```sh
        pip3 install luciferase
        ```
        or
        ```sh
        pip3 install --user luciferase
        ```
        
        ## Command-line interface for barplots
        
        ### Barplots of enhancer activity
        
        A script called `luciferase-barplot` for creating bar plots from JSON-formatted
        data is included. After installing `luciferase`, you can use it like this:
        ```sh
        luciferase-barplot --title "plot title" example.json example.pdf 
        ```
        
        See also the help message:
        ```sh
        luciferase-barplot -h
        ```
        
        Examples of luciferase reporter data in JSON format:
        ```json
        {
          "Non-risk, Fwd": [8.354, 12.725, 8.506],
          "Risk, Fwd": [5.078, 5.038, 5.661],
          "Non-risk, Rev": [9.564, 9.692, 12.622],
          "Risk, Rev": [10.777, 11.389, 10.598],
          "Empty": [1.042, 0.92, 1.042]
        }
        ```
        ```json
        {
          "Alt, MIN6": [5.47, 7.17, 6.15],
          "Ref, MIN6": [3.16, 3.04, 4.34],
          "Empty, MIN6": [1.07, 0.83, 0.76],
          "Alt, ALPHA-TC6": [2.50, 3.47, 3.33],
          "Ref, ALPHA-TC6": [2.01, 1.96, 2.31],
          "Empty, ALPHA-TC6": [1.042, 0.92, 1.042]
        }
        ```
        
        The input JSON should contain either five, six, or twelve entries. If it
        contains five entries, the bars of the resulting plot will have a 2-2-1 style.
        If it contains six entries, the bars will have a 2-1-2-1 style. If twelve,
        the syle will be as with six entries but doubled.
        
        Significance indicators will be written above the bars: `***` if p<0.001,
        `**` if p<0.01, `*` if p<0.05, `ns` otherwise.
        
        Here is an example of a plot in the 2-1-2-1 style:
        
        ![example barplot](https://github.com/anthony-aylward/islet-cytokines-outline/raw/master/figure/rs3787186_luc/dex_vs_untreated.png)
        
        
        ### Barplots of allelic ratio
        
        A second script called `luciferase-ratioplot` takes the same input data and
        produces a comparative plot of allelic ratios:
        
        ```sh
        luciferase-ratioplot --title "plot title" example.json example.pdf
        ```
        
        For this script, the number of entries in the input JSON should be a multiple
        of 3. The resulting plot shows the estimated allelic ratio of enhancer activity
        with confidence intervals (95% by default). Here is an example input dataset
        and plot:
        
        ```
        {
          "Alt, dex": [44.6, 37.6, 37.7],
          "Ref, dex": [149.4, 99.7, 124.5],
          "Empty, dex": [1.1, 1.0, 0.9],
          "Alt, untreated": [19.7, 16.2, 18.3],
          "Ref, untreated": [33.2, 30.3, 33.3],
          "Empty, untreated": [1.0, 1.0, 1.0]
        }
        ```
        ![example ratio plot](https://github.com/anthony-aylward/luciferase/raw/master/example/ratio.png)
        
        ## Meta-analysis of luciferase reporter data
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
