scez 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

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Files changed (6) hide show
  1. pyproject.toml +45 -0
  2. scez/diffexp.py +4 -3
  3. {scez-0.1.1.dist-info → scez-0.1.2.dist-info}/METADATA +3 -2
  4. {scez-0.1.1.dist-info → scez-0.1.2.dist-info}/RECORD +6 -5
  5. {scez-0.1.1.dist-info → scez-0.1.2.dist-info}/WHEEL +1 -1
  6. {scez-0.1.1.dist-info → scez-0.1.2.dist-info}/LICENSE +0 -0
pyproject.toml ADDED
@@ -0,0 +1,45 @@
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+ [tool.poetry]
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+ name = "scez"
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+ version = "0.1.2"
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+ authors = [
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+ "Abe Arab <abarbiology@gmail.com>"
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+ ]
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+ license = "MIT"
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+ readme = "README.md"
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+ description = "Single Cell Analysis, Easy Mode!"
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+ classifiers = [
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+ "License :: OSI Approved :: MIT License"
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+ ]
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+ packages = [
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+ { include = "scez" },
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+ { include = "pyproject.toml" },
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+ ]
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+
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+ [tool.poetry.urls]
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+ Source = "https://github.com/abearab/scez"
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+
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+ [tool.poetry.dependencies]
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+ python = "^3.9 <4.0"
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+ numpy = "^1.26.0"
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+ pandas = "^2.1.4 <3.0.0"
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+ bottleneck = "^1.3.6"
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+ tqdm = "*"
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+ tomli = "*"
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+ matplotlib = "^3.7"
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+ seaborn = "^0.12.2"
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+ adjustText = "^0.7.3"
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+ scanpy = "^1.9.6"
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+ anndata = "^0.8.0"
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+ adpbulk = "^0.1.4"
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+ pydeseq2 = "^0.4.0"
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+ pytdc = "^1.0.0"
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+ blitzgsea = "^1.3.0"
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+
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+
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+ [tool.poetry.group.test.dependencies]
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+ pytest = "*"
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+ tomli = "*"
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+
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+ [build-system]
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+ requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
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+ build-backend = "poetry_dynamic_versioning.backend"
scez/diffexp.py CHANGED
@@ -136,7 +136,8 @@ def plot_volcano(df, title=None, labels=None, n_genes=False, side='both',
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  plt.show()
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- def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, side='both', font_scale=1, figsize=(10, 4), **kwargs):
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+ 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):
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+
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  label_font_size = 9 * font_scale
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  title_font_size = 10 * font_scale
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@@ -167,11 +168,11 @@ def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, s
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  selected_genes = df.nlargest(n_genes, '-log10(pvalue)')
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  # Filter the single-cell dataset for the selected genes
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- subset_adata = adata[:, selected_genes.index]
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+ subset_adata = adata[:, selected_genes.index].copy()
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  subset_adata.var.index = subset_adata.var.index.str.split('_').str[0]
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  # Convert the subset of adata to a DataFrame
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- subset_df = subset_adata.to_df()
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+ subset_df = subset_adata.to_df(layer=layer)
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  # Merge the DataFrame with .obs to include the 'sample' information
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  merged_df = pd.merge(subset_df, adata.obs[['sample']], left_index=True, right_index=True)
{scez-0.1.1.dist-info → scez-0.1.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.3
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  Name: scez
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- Version: 0.1.1
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+ Version: 0.1.2
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  Summary: Single Cell Analysis, Easy Mode!
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  License: MIT
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  Author: Abe Arab
@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3.9
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  Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
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  Requires-Dist: adjustText (>=0.7.3,<0.8.0)
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  Requires-Dist: adpbulk (>=0.1.4,<0.2.0)
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  Requires-Dist: anndata (>=0.8.0,<0.9.0)
{scez-0.1.1.dist-info → scez-0.1.2.dist-info}/RECORD RENAMED
@@ -1,11 +1,12 @@
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+ pyproject.toml,sha256=2d1qGZM5rM0Jttr_6ZTfqe0VX6qF200vJvtIQcAZN-E,900
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  scez/__init__.py,sha256=3zXd7gUTFNJK-_l89LYFI-8yqkjt99dYLmZozK6qk0c,1412
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- scez/diffexp.py,sha256=V8qjqpTZVaoAb-iCa3jYmPDmDBtg5AK9OqNzRow6ic0,6770
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+ scez/diffexp.py,sha256=q76lqldFa4_fWNmx3I1xpnurZ6drbJAIZKXf3MHVw_A,6805
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  scez/preprocess.py,sha256=3iaxACkmKQjKZdaFBLRAXz1kwkNnhbdnd_gwF8rI4nw,2572
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  scez/representation.py,sha256=IW0pwa_yoKf-2a3lbtxRwLTdCjB2PkS9oN4WGCLwED0,1596
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  scez/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  scez/tests/test_scez.py,sha256=hoBSYB5k1WtF1hY_kyWXw1W7NolBornmTdAng6tDpjw,452
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  scez/utils.py,sha256=lPmt01JILiKoBUhhxZeyhl2CfAzailTp4dIefP4FqGQ,1955
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- scez-0.1.1.dist-info/LICENSE,sha256=59TS1D5RmGh66RJikXvFoq_ZW9pGirB4zUOUXLfptJM,1071
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- scez-0.1.1.dist-info/METADATA,sha256=RzrXbfCm1W6Nt5s55S54YDb-XWW2WOq7P482DG3tSf4,2930
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- scez-0.1.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- scez-0.1.1.dist-info/RECORD,,
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+ scez-0.1.2.dist-info/LICENSE,sha256=59TS1D5RmGh66RJikXvFoq_ZW9pGirB4zUOUXLfptJM,1071
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+ scez-0.1.2.dist-info/METADATA,sha256=tRmPIrFKlzcb09QVpyEoU0meDAYzrZ7_0RlUd4cfTtI,2981
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+ scez-0.1.2.dist-info/WHEEL,sha256=RaoafKOydTQ7I_I3JTrPCg6kUmTgtm4BornzOqyEfJ8,88
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+ scez-0.1.2.dist-info/RECORD,,
{scez-0.1.1.dist-info → scez-0.1.2.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: poetry-core 1.9.0
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+ Generator: poetry-core 2.0.0
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  Root-Is-Purelib: true
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  Tag: py3-none-any
{scez-0.1.1.dist-info → scez-0.1.2.dist-info}/LICENSE RENAMED
File without changes