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Add functions for integrating CITE-seq data #114

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Add functions for integrating CITE-seq data #114

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6d7d841
integrate citeseq
HelloWorldLTY Feb 4, 2024
55ad68d
update p
HelloWorldLTY Feb 5, 2024
927d77b
update computation of nbmixture
HelloWorldLTY Feb 5, 2024
45cada0
modify the codes
HelloWorldLTY Feb 23, 2024
3923df9
update utils
HelloWorldLTY Feb 23, 2024
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78 changes: 78 additions & 0 deletions .history/pyproject_20240208235548.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
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[build-system]
requires = ["setuptools", "wheel", "flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "scglue"
version = "0.3.2"
description = "Graph-linked unified embedding for unpaired single-cell multi-omics data integration"
readme = "README.md"
requires-python = ">=3.6"
license = {file = "LICENSE"}
authors = [
{name = "Zhi-Jie Cao", email = "caozj@mail.cbi.pku.edu.cn"},
{name = "Xin-Ming Tu", email = "xinmingtu@pku.edu.cn"}
]
keywords = ["bioinformatics", "deep-learning", "single-cell", "single-cell-multiomics"]
classifiers = [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
dependencies = [
"numpy>=1.19",
"scipy>=1.3",
"pandas>=1.1",
"matplotlib>=3.1.2",
"seaborn>=0.9",
"dill>=0.2.3",
"tqdm>=4.27",
"scikit-learn>=0.21.2",
"statsmodels>=0.10",
"parse>=1.3.2",
"networkx>=2",
"pynvml>=8.0.1",
"torch>=1.8",
"pytorch-ignite>=0.4.1",
"tensorboardX>=1.4",
"anndata>=0.7",
"scanpy>=1.5",
"pybedtools>=0.8.1",
"h5py>=2.10",
"sparse>=0.3.1",
"packaging>=16.8",
"leidenalg>=0.7",
"muon>=0.1.5"
]

[project.optional-dependencies]
doc = [
"sphinx<7",
"sphinx-autodoc-typehints",
"sphinx-copybutton",
"sphinx-intl",
"nbsphinx",
"sphinx-rtd-theme",
"ipython",
"jinja2"
]
test = [
"plotly",
"pytest",
"pytest-cov"
]

[project.urls]
Github = "https://github.com/gao-lab/GLUE"

[tool.flit.sdist]
exclude = [".*", "c*", "d*", "e*", "pa*", "t*", "T*"]
78 changes: 78 additions & 0 deletions .history/pyproject_20240223082542.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
[build-system]
requires = ["setuptools", "wheel", "flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "scglue"
version = "0.3.2"
description = "Graph-linked unified embedding for unpaired single-cell multi-omics data integration"
readme = "README.md"
requires-python = ">=3.6"
license = {file = "LICENSE"}
authors = [
{name = "Zhi-Jie Cao", email = "caozj@mail.cbi.pku.edu.cn"},
{name = "Xin-Ming Tu", email = "xinmingtu@pku.edu.cn"}
]
keywords = ["bioinformatics", "deep-learning", "single-cell", "single-cell-multiomics"]
classifiers = [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
dependencies = [
"numpy>=1.19",
"scipy>=1.3",
"pandas>=1.1",
"matplotlib>=3.1.2",
"seaborn>=0.9",
"dill>=0.2.3",
"tqdm>=4.27",
"scikit-learn>=0.21.2",
"statsmodels>=0.10",
"parse>=1.3.2",
"networkx>=2",
"pynvml>=8.0.1",
"torch>=1.8",
"pytorch-ignite>=0.4.1",
"tensorboardX>=1.4",
"anndata>=0.7",
"scanpy>=1.5",
"pybedtools>=0.8.1",
"h5py>=2.10",
"sparse>=0.3.1",
"packaging>=16.8",
"leidenalg>=0.7",
"muon>=0.1.5"
]

[project.optional-dependencies]
doc = [
"sphinx<7",
"sphinx-autodoc-typehints",
"sphinx-copybutton",
"sphinx-intl",
"nbsphinx",
"sphinx-rtd-theme",
"ipython",
"jinja2"
]
test = [
"plotly",
"pytest",
"pytest-cov"
]

[project.urls]
Github = "https://github.com/gao-lab/GLUE"

[tool.flit.sdist]
exclude = [".*", "c*", "d*", "e*", "pa*", "t*", "T*"]
78 changes: 78 additions & 0 deletions .history/pyproject_20240223083721.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
[build-system]
requires = ["setuptools", "wheel", "flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "scglue"
version = "0.3.2"
description = "Graph-linked unified embedding for unpaired single-cell multi-omics data integration"
readme = "README.md"
requires-python = ">=3.6"
license = {file = "LICENSE"}
authors = [
{name = "Zhi-Jie Cao", email = "caozj@mail.cbi.pku.edu.cn"},
{name = "Xin-Ming Tu", email = "xinmingtu@pku.edu.cn"}
]
keywords = ["bioinformatics", "deep-learning", "single-cell", "single-cell-multiomics"]
classifiers = [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
dependencies = [
"numpy>=1.19",
"scipy>=1.3",
"pandas>=1.1",
"matplotlib>=3.1.2",
"seaborn>=0.9",
"dill>=0.2.3",
"tqdm>=4.27",
"scikit-learn>=0.21.2",
"statsmodels>=0.10",
"parse>=1.3.2",
"networkx>=2",
"pynvml>=8.0.1",
"torch>=1.8",
"pytorch-ignite>=0.4.1",
"tensorboardX>=1.4",
"anndata>=0.7",
"scanpy>=1.5",
"pybedtools>=0.8.1",
"h5py>=2.10",
"sparse>=0.3.1",
"packaging>=16.8",
"leidenalg>=0.7",
"muon>=0.1.5"
]

[project.optional-dependencies]
doc = [
"sphinx<7",
"sphinx-autodoc-typehints",
"sphinx-copybutton",
"sphinx-intl",
"nbsphinx",
"sphinx-rtd-theme",
"ipython",
"jinja2"
]
test = [
"plotly",
"pytest",
"pytest-cov"
]

[project.urls]
Github = "https://github.com/gao-lab/GLUE"

[tool.flit.sdist]
exclude = [".*", "c*", "d*", "e*", "pa*", "t*", "T*"]
78 changes: 78 additions & 0 deletions .history/pyproject_20240223083840.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
[build-system]
requires = ["setuptools", "wheel", "flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "scglue"
version = "0.3.2"
description = "Graph-linked unified embedding for unpaired single-cell multi-omics data integration"
readme = "README.md"
requires-python = ">=3.6"
license = {file = "LICENSE"}
authors = [
{name = "Zhi-Jie Cao", email = "caozj@mail.cbi.pku.edu.cn"},
{name = "Xin-Ming Tu", email = "xinmingtu@pku.edu.cn"}
]
keywords = ["bioinformatics", "deep-learning", "single-cell", "single-cell-multiomics"]
classifiers = [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
dependencies = [
"numpy>=1.19",
"scipy>=1.3",
"pandas>=1.1",
"matplotlib>=3.1.2",
"seaborn>=0.9",
"dill>=0.2.3",
"tqdm>=4.27",
"scikit-learn>=0.21.2",
"statsmodels>=0.10",
"parse>=1.3.2",
"networkx>=2",
"pynvml>=8.0.1",
"torch>=1.8",
"pytorch-ignite>=0.4.1",
"tensorboardX>=1.4",
"anndata>=0.7",
"scanpy>=1.5",
"pybedtools>=0.8.1",
"h5py>=2.10",
"sparse>=0.3.1",
"packaging>=16.8",
"leidenalg>=0.7",
"muon>=0.1.5"
]

[project.optional-dependencies]
doc = [
"sphinx<7",
"sphinx-autodoc-typehints",
"sphinx-copybutton",
"sphinx-intl",
"nbsphinx",
"sphinx-rtd-theme",
"ipython",
"jinja2"
]
test = [
"plotly",
"pytest",
"pytest-cov"
]

[project.urls]
Github = "https://github.com/gao-lab/GLUE"

[tool.flit.sdist]
exclude = [".*", "c*", "d*", "e*", "pa*", "t*", "T*"]
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