Merge pull request #84 from ArcInstitute/dev

improvements in phenotype calculation

docs/source/history.rst

@@ -10,6 +10,7 @@ History
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 * add command line interface, i.e. ``screenpro --help``
 * rename ``Counter`` class to ``GuideCounter`` for code clarity
+* key bug fixes and improvements in phenotype calculation, normalization, and statistics
 * major bug fixes and improvements in code formatting
 
 0.2.11 - 0.3.5 (Apr 2024 - June 2024)

docs/source/ngs.md

@@ -17,14 +17,14 @@ used for the screen, the functions are divided into two classes:
 
 ### Cas9 CRISPR-Cas system (single or dual sgRNA libraries)
 ```{eval-rst}  
-.. automodule:: screenpro.cas9
+.. automodule:: screenpro.ngs.cas9
    :members:
    :show-inheritance:
 ```
 
 ### Cas12 CRISPR-Cas system (multiplexed crRNA libraries)
 ```{eval-rst}  
-.. automodule:: screenpro.cas12
+.. automodule:: screenpro.ngs.cas12
    :members:
    :show-inheritance:
 ```

docs/source/visualize.md

@@ -1,12 +1,22 @@
-# Visualize module
+# Visualization modules
 
 Set of python classes and functions to enable visualizing CRISPR screening datasets.
 
 ___
 
 ```{eval-rst}  
-.. automodule:: screenpro.visualize
+.. automodule:: screenpro.plotting.qc_plots
    :members:
    :undoc-members:
    :show-inheritance:
-```
+
+.. automodule:: screenpro.plotting.pheno_plots
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: screenpro.dashboard
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```

environment.yml

@@ -21,8 +21,8 @@ dependencies:
   - pip
   - pip:
       - polars
-      - pyarrow<17.0
-      - biobear>=0.20.3,<0.21
+      - pyarrow
+      - biobear
       - numba
       - pydeseq2
       - simple_colors

screenpro/__init__.py

@@ -31,6 +31,6 @@
 from .dashboard import DrugScreenDashboard
 
 
-__version__ = "0.4.6"
+__version__ = "0.4.7"
 __author__ = "Abe Arab"
 __email__ = '[email protected]' # "[email protected]"