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@@ -0,0 +1 @@ +/SpaDecon-1.1.2.tar.gz diff --git a/python-spadecon.spec b/python-spadecon.spec new file mode 100644 index 0000000..1c97858 --- /dev/null +++ b/python-spadecon.spec @@ -0,0 +1,251 @@ +%global _empty_manifest_terminate_build 0 +Name: python-SpaDecon +Version: 1.1.2 +Release: 1 +Summary: SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning +License: MIT License +URL: https://github.com/kylepcoleman87/SpaDecon +Source0: https://mirrors.aliyun.com/pypi/web/packages/fa/a0/96e2f8fba0e577948f7e7e948f31aa619968bd1ce0861f94ff392c341826/SpaDecon-1.1.2.tar.gz +BuildArch: noarch + +Requires: python3-keras +Requires: python3-pandas +Requires: python3-numpy +Requires: python3-scipy +Requires: python3-scanpy +Requires: python3-anndata +Requires: python3-sklearn +Requires: python3-tensorflow + +%description +# SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning + +### Kyle Coleman, Jian Hu, Amelia Schroeder, Edward B. Lee, Mingyao Li* + +SpaDecon is a semi-supervised learning-based method developed to perform cell-type deconvolution on spatially resolved transcriptomics (SRT) datasets. SpaDecon has been shown to provide accurate cell-type deconvolution results for both Spatial Transcriptomics (ST) and 10X Visium SRT datasets. Annotated scRNA-seq gene expression data from the same type of tissue as the SRT data are required for deconvolution. + + + +## SpaDecon Installation +- SpaDecon installation requires a python version of at least 3.6. The version of python can be checked by: +```python +import platform +platform.python_version() +``` + + '3.7.11' + +We recommend creating and activating a new conda environment when installing the SpaDecon package. For instance, +```bash +conda create -n SpaDecon python=3.7 +conda activate SpaDecon +``` + +There are mulitple ways to install SpaDecon: + +- Install SpaDecon using PyPI: + +```bash +pip3 install SpaDecon +``` + +- Download and install SpaDecon package from GitHub: + +```bash +git clone https://github.com/kpcoleman/SpaDecon +cd SpaDecon/ +python3 setup.py install --user +``` + +## Tutorial +A markdown tutorial file can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/Tutorial.md + +A tutorial in the form of a jupyter notebook can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/tutorial.ipynb + + + +## Software Requirements +python >= 3.6 +keras==2.2.4 +pandas==1.2.4 +numpy==1.20.1 +scipy==1.6.2 +scanpy==1.7.0 +anndata==0.7.6 +sklearn +tensorflow==1.14.0 + + + +%package -n python3-SpaDecon +Summary: SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning +Provides: python-SpaDecon +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-SpaDecon +# SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning + +### Kyle Coleman, Jian Hu, Amelia Schroeder, Edward B. Lee, Mingyao Li* + +SpaDecon is a semi-supervised learning-based method developed to perform cell-type deconvolution on spatially resolved transcriptomics (SRT) datasets. SpaDecon has been shown to provide accurate cell-type deconvolution results for both Spatial Transcriptomics (ST) and 10X Visium SRT datasets. Annotated scRNA-seq gene expression data from the same type of tissue as the SRT data are required for deconvolution. + + + +## SpaDecon Installation +- SpaDecon installation requires a python version of at least 3.6. The version of python can be checked by: +```python +import platform +platform.python_version() +``` + + '3.7.11' + +We recommend creating and activating a new conda environment when installing the SpaDecon package. For instance, +```bash +conda create -n SpaDecon python=3.7 +conda activate SpaDecon +``` + +There are mulitple ways to install SpaDecon: + +- Install SpaDecon using PyPI: + +```bash +pip3 install SpaDecon +``` + +- Download and install SpaDecon package from GitHub: + +```bash +git clone https://github.com/kpcoleman/SpaDecon +cd SpaDecon/ +python3 setup.py install --user +``` + +## Tutorial +A markdown tutorial file can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/Tutorial.md + +A tutorial in the form of a jupyter notebook can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/tutorial.ipynb + + + +## Software Requirements +python >= 3.6 +keras==2.2.4 +pandas==1.2.4 +numpy==1.20.1 +scipy==1.6.2 +scanpy==1.7.0 +anndata==0.7.6 +sklearn +tensorflow==1.14.0 + + + +%package help +Summary: Development documents and examples for SpaDecon +Provides: python3-SpaDecon-doc +%description help +# SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning + +### Kyle Coleman, Jian Hu, Amelia Schroeder, Edward B. Lee, Mingyao Li* + +SpaDecon is a semi-supervised learning-based method developed to perform cell-type deconvolution on spatially resolved transcriptomics (SRT) datasets. SpaDecon has been shown to provide accurate cell-type deconvolution results for both Spatial Transcriptomics (ST) and 10X Visium SRT datasets. Annotated scRNA-seq gene expression data from the same type of tissue as the SRT data are required for deconvolution. + + + +## SpaDecon Installation +- SpaDecon installation requires a python version of at least 3.6. The version of python can be checked by: +```python +import platform +platform.python_version() +``` + + '3.7.11' + +We recommend creating and activating a new conda environment when installing the SpaDecon package. For instance, +```bash +conda create -n SpaDecon python=3.7 +conda activate SpaDecon +``` + +There are mulitple ways to install SpaDecon: + +- Install SpaDecon using PyPI: + +```bash +pip3 install SpaDecon +``` + +- Download and install SpaDecon package from GitHub: + +```bash +git clone https://github.com/kpcoleman/SpaDecon +cd SpaDecon/ +python3 setup.py install --user +``` + +## Tutorial +A markdown tutorial file can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/Tutorial.md + +A tutorial in the form of a jupyter notebook can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/tutorial.ipynb + + + +## Software Requirements +python >= 3.6 +keras==2.2.4 +pandas==1.2.4 +numpy==1.20.1 +scipy==1.6.2 +scanpy==1.7.0 +anndata==0.7.6 +sklearn +tensorflow==1.14.0 + + + +%prep +%autosetup -n SpaDecon-1.1.2 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-SpaDecon -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 1.1.2-1 +- Package Spec generated @@ -0,0 +1 @@ +46c5b3bccb52c2fb76c55aaa757479ec SpaDecon-1.1.2.tar.gz |