Merge pull request #54 from ArcInstitute/cli

minor changes in docs

README.md

@@ -1,30 +1,19 @@
 [![website](https://img.shields.io/badge/website-live-brightgreen)](https://arcinstitute.org/tools/screenpro2)
-![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)
+![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)](https://pepy.tech/project/screenpro2)
 [![Downloads](https://static.pepy.tech/badge/screenpro2/month)](https://pepy.tech/project/screenpro2)
 [![CodeQL](https://github.com/ArcInstitute/ScreenPro2/actions/workflows/github-code-scanning/codeql/badge.svg)](https://github.com/ArcInstitute/ScreenPro2/actions/workflows/github-code-scanning/codeql)
 # ScreenPro2
 
+## TL;DR
 
-The complete docs are available at [screenpro2.rtfd.io](https://screenpro2.readthedocs.io).
+[ReadTheDocs](https://screenpro2.readthedocs.io) |
+[PyPI](https://pypi.org/project/ScreenPro2)
 
-## Table of Contents
-- [Installation](#installation)
-- [Usage](#usage)
-  * [Step 1: FASTQ to counts](#step-1-fastq-to-counts)
-  * [Step 2: Phenotype calculation](#step-2-phenotype-calculation)
-    + [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)
-  * [Step 3: Explore results and QC reports](#step-3-explore-results-and-qc-reports)
-
-- [Supported CRISPR Screen Platforms](#supported-crispr-screen-platforms)
-  * [dCas9 CRISPRa/i single-sgRNA screens](#dcas9-crispra/i-single-sgrna-screens)
-  * [dCas9 CRISPRa/i dual-sgRNA screens](#dcas9-crispra/i-dual-sgrna-screens)
-  <!-- * [multiCas12a CRISPRi screens](#multicas12a-crispri-screens) -->
-- [License](#license)
-- [Citation](#citation)
+ScreenPro2 is tool to perform flexible analysis on high-content CRISPR screening datasets. It has functionalities to process data from diverse CRISPR screen platforms and is designed to be modular to enable easy extension to custom CRISPR screen platforms or other commonly used platforms in addition to the ones currently implemented.
 
+___
 ## Introduction
 Functional genomics field is evolving rapidly and many more CRISPR screen platforms are now developed. Therefore, 
 it's important to have a standardized workflow to analyze the data from these screens. ScreenPro2 is provided to 

docs/source/index.rst

@@ -16,6 +16,7 @@ Welcome to ScreenPro2's documentation!
    assays
    ngs
    phenotype
+   plotting
    load
 
 .. toctree::

docs/source/ngs.rst

@@ -1,7 +1,11 @@
 NGS screen processing module
 =======================
 
-Set of python functions to process and analyze NGS files from CRISPR screens.
+`Counter` class is a wrapper to run the functions for a CRISPR screen experiment.
+
+This module contains a set of python functions to process and analyze NGS files from CRISPR screens.
+Based on the type of CRISPR-Cas system used for the screen, the functions are divided into 
+two classes: `Cas9` and `Cas12`.
 
 -----------------------
 
@@ -10,6 +14,11 @@ Set of python functions to process and analyze NGS files from CRISPR screens.
    :undoc-members:
    :show-inheritance:
 
+.. automodule:: screenpro.ngs.counter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 .. automodule:: screenpro.ngs.cas9
    :members:
    :undoc-members:

docs/source/phenotype.rst

@@ -58,11 +58,5 @@ Statistical test comparing :math:`y` vs :math:`x` per each target, :math:`T`:
    :undoc-members:
    :show-inheritance:
 
-.. automodule:: screenpro.plotting
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
 .. _`Dependent t-test for paired samples`: https://en.wikipedia.org/wiki/Student%27s_t-test#Dependent_t-test_for_paired_samples
 .. _`ttest_rel, a scipy module`: https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_rel.html

docs/source/plotting.rst

@@ -0,0 +1,9 @@
+Plotting and visualization modules
+=======================
+
+
+.. automodule:: screenpro.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+