scez 0.1.0__tar.gz → 0.1.2__tar.gz

{scez-0.1.0 → scez-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: scez
-Version: 0.1.0
+Version: 0.1.2
 Summary: Single Cell Analysis, Easy Mode!
 License: MIT
 Author: Abe Arab
@@ -12,22 +12,36 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: adjustText (>=0.7.3,<0.8.0)
 Requires-Dist: adpbulk (>=0.1.4,<0.2.0)
-Requires-Dist: anndata (>=0.7.4,<0.8.0)
+Requires-Dist: anndata (>=0.8.0,<0.9.0)
 Requires-Dist: blitzgsea (>=1.3.0,<2.0.0)
+Requires-Dist: bottleneck (>=1.3.6,<2.0.0)
 Requires-Dist: matplotlib (>=3.7,<4.0)
-Requires-Dist: numpy (>=1.17.0,<2.0.0)
-Requires-Dist: pandas (>=0.21,<0.22)
+Requires-Dist: numpy (>=1.26.0,<2.0.0)
+Requires-Dist: pandas (>=2.1.4,<3.0.0)
 Requires-Dist: pydeseq2 (>=0.4.0,<0.5.0)
 Requires-Dist: pytdc (>=1.0.0,<2.0.0)
+Requires-Dist: scanpy (>=1.9.6,<2.0.0)
 Requires-Dist: seaborn (>=0.12.2,<0.13.0)
+Requires-Dist: tomli
 Requires-Dist: tqdm
 Project-URL: Source, https://github.com/abearab/scez
 Description-Content-Type: text/markdown
 
 ## scez – single cell, easy mode
 [![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
+[![PyPI version](https://badge.fury.io/py/scez.svg)](https://badge.fury.io/py/scez)
+[![Downloads](https://static.pepy.tech/badge/scez)](https://pepy.tech/project/scez)
+[![Downloads](https://static.pepy.tech/badge/scez/month)](https://pepy.tech/project/scez)
+
+
+### Description
+There are many tools available for single-cell RNA-seq analysis, but they often require a lot of understanding of the underlying algorithms, reading of documentation, and setting up analysis environments. This takes time and effort, and can be a barrier to entry for many projects. [Single-Cell Best Practices](https://github.com/theislab/single-cell-best-practices) is a great resource for learning about the best practices for single-cell analysis. `scez` aims to provide functionalities for single-cell analysis through definitions of analysis "tasks" and implementation of these "best practices" in a user-friendly way.
+
+This is more a personal effort to streamline my own analysis workflows, but I hope it can be useful to others as well.
+
 
 ### Installation
 Make sure you have mamba installed in your base environment. If not, install it with:
@@ -36,7 +50,7 @@ conda install mamba -n base -c conda-forge
 ```
 Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
 ```bash
-conda env create -f environment.yml
+conda env create -f https://raw.githubusercontent.com/abearab/scez/main/environment.yml
 
 conda activate scez
 ```
@@ -46,6 +60,7 @@ Finally, install scez with:
 pip install scez
 ```
 
+___
 Or, if you want to install the latest version from the repository:
 ```bash
 pip install git+https://github.com/abearab/scez.git

scez-0.1.2/README.md

@@ -0,0 +1,35 @@
+## scez – single cell, easy mode
+[![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
+[![PyPI version](https://badge.fury.io/py/scez.svg)](https://badge.fury.io/py/scez)
+[![Downloads](https://static.pepy.tech/badge/scez)](https://pepy.tech/project/scez)
+[![Downloads](https://static.pepy.tech/badge/scez/month)](https://pepy.tech/project/scez)
+
+
+### Description
+There are many tools available for single-cell RNA-seq analysis, but they often require a lot of understanding of the underlying algorithms, reading of documentation, and setting up analysis environments. This takes time and effort, and can be a barrier to entry for many projects. [Single-Cell Best Practices](https://github.com/theislab/single-cell-best-practices) is a great resource for learning about the best practices for single-cell analysis. `scez` aims to provide functionalities for single-cell analysis through definitions of analysis "tasks" and implementation of these "best practices" in a user-friendly way.
+
+This is more a personal effort to streamline my own analysis workflows, but I hope it can be useful to others as well.
+
+
+### Installation
+Make sure you have mamba installed in your base environment. If not, install it with:
+```bash
+conda install mamba -n base -c conda-forge
+```
+Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
+```bash
+conda env create -f https://raw.githubusercontent.com/abearab/scez/main/environment.yml
+
+conda activate scez
+```
+Finally, install scez with:
+
+```bash
+pip install scez
+```
+
+___
+Or, if you want to install the latest version from the repository:
+```bash
+pip install git+https://github.com/abearab/scez.git
+```

{scez-0.1.0 → scez-0.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "scez"
-version = "0.1.0"
+version = "0.1.2"
 authors = [
 	"Abe Arab <abarbiology@gmail.com>"
 ]
@@ -12,6 +12,7 @@ classifiers = [
 ]
 packages = [
 	{ include = "scez" },
+	{ include = "pyproject.toml" },
 ]
 
 [tool.poetry.urls]
@@ -19,17 +20,20 @@ Source = "https://github.com/abearab/scez"
 
 [tool.poetry.dependencies]
 python = "^3.9 <4.0"
-anndata = "^0.7.4"
-numpy = "^1.17.0"
-pandas = "^0.21 <2.0"
+numpy = "^1.26.0"
+pandas = "^2.1.4 <3.0.0"
+bottleneck = "^1.3.6"
+tqdm = "*"
+tomli = "*"
 matplotlib = "^3.7"
 seaborn = "^0.12.2"
 adjustText = "^0.7.3"
+scanpy = "^1.9.6"
+anndata = "^0.8.0"
 adpbulk  = "^0.1.4"
 pydeseq2 = "^0.4.0"
 pytdc = "^1.0.0"
 blitzgsea = "^1.3.0"
-tqdm = "*"
 
 
 [tool.poetry.group.test.dependencies]

{scez-0.1.0 → scez-0.1.2}/scez/__init__.py

@@ -8,8 +8,9 @@ import scanpy as sc
 import matplotlib.pyplot as plt
 
 import tomli
+from pathlib import Path
 
-toml_dict = tomli.load(open('pyproject.toml','rb'))
+toml_dict = tomli.load(open(Path(__file__).parent.parent / 'pyproject.toml','rb'))
 __version__ = toml_dict['tool']['poetry']['version']
 
 

{scez-0.1.0 → scez-0.1.2}/scez/diffexp.py

@@ -136,7 +136,8 @@ def plot_volcano(df, title=None, labels=None, n_genes=False, side='both',
         plt.show()
 
 
-def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, side='both', font_scale=1, figsize=(10, 4), **kwargs):
+def plot_top_DEG_violinplot(adata, df, layer=None, title=None, labels=None, n_genes=False, side='both', font_scale=1, figsize=(10, 4), **kwargs):
+    
     label_font_size = 9 * font_scale
     title_font_size = 10 * font_scale
 
@@ -167,11 +168,11 @@ def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, s
         selected_genes = df.nlargest(n_genes, '-log10(pvalue)')
 
     # Filter the single-cell dataset for the selected genes
-    subset_adata = adata[:, selected_genes.index]
+    subset_adata = adata[:, selected_genes.index].copy()
     subset_adata.var.index = subset_adata.var.index.str.split('_').str[0]
 
     # Convert the subset of adata to a DataFrame
-    subset_df = subset_adata.to_df()
+    subset_df = subset_adata.to_df(layer=layer)
 
     # Merge the DataFrame with .obs to include the 'sample' information
     merged_df = pd.merge(subset_df, adata.obs[['sample']], left_index=True, right_index=True)

scez-0.1.0/README.md

@@ -1,24 +0,0 @@
-## scez – single cell, easy mode
-[![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
-
-### Installation
-Make sure you have mamba installed in your base environment. If not, install it with:
-```bash
-conda install mamba -n base -c conda-forge
-```
-Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
-```bash
-conda env create -f environment.yml
-
-conda activate scez
-```
-Finally, install scez with:
-
-```bash
-pip install scez
-```
-
-Or, if you want to install the latest version from the repository:
-```bash
-pip install git+https://github.com/abearab/scez.git
-```