diff options
| author | CoprDistGit <infra@openeuler.org> | 2023-05-15 05:11:23 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-15 05:11:23 +0000 |
| commit | 9e8960b5f4f9c176b881f11ccb5bb45c5ec8940a (patch) | |
| tree | c105e5deb91369e4ea43db7df9397130118d118c | |
| parent | 67bd91ca18bbe229df48ed24ce1f4494326bedfb (diff) | |
automatic import of python-congas
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-congas.spec | 200 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 202 insertions, 0 deletions
@@ -0,0 +1 @@ +/congas-0.0.75.tar.gz diff --git a/python-congas.spec b/python-congas.spec new file mode 100644 index 0000000..7ff0320 --- /dev/null +++ b/python-congas.spec @@ -0,0 +1,200 @@ +%global _empty_manifest_terminate_build 0 +Name: python-congas +Version: 0.0.75 +Release: 1 +Summary: Copy Number genotyping from single cell RNA sequencing +License: GPL-3.0 +URL: https://github.com/Militeee/congas +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/0b/81/40cafaca7406d60c112f93d1ea0bc0208cfa06667f5b1ef0510bd26eb7fc/congas-0.0.75.tar.gz +BuildArch: noarch + +Requires: python3-matplotlib +Requires: python3-pandas +Requires: python3-pyro-ppl +Requires: python3-numpy +Requires: python3-scikit-learn + +%description +# Copy number genotyping from scRNA sequencing + + +[](https://travis-ci.org/Militeee/congas) +[](https://codecov.io/gh/Militeee/congas) + + +A set of Pyro models and functions to infer CNA from scRNA-seq data. +It comes with a companion R package (hlink) that works as an interface and provides preprocessing, simulation and visualization routines. + + +Currently providing: + +- A mixture model on segments where CNV are modelled as LogNormal random variable (MixtureGaussian) +- Same as above but the number of cluster is learned (MixtureGaussianDMP) +- A model where CNVs are modelled as outcome from Categorical distributions, clusters share the same parameters (MixtureDirichlet) +- A simple Hmm where CNVs are again categorical, but there is no clustering (SimpleHmm) +- The version of MixtureDirichlet but with temporal dependency (HmmMixtureRNA) + +Coming soon: +- A linear model in the emission that can account for known covariates +- The equivalent of MixtureGaussian but with CNVs as Categorical random variable +- A model on genes (all the other models assume a division in segments) + +To install: + +`$ pip install congas` + +To run a simple analysis on the example data + +```python +import congas as cn +from congas.models import MixtureGaussian +data_dict = cn.simulation_data +params, loss = cn.run_analysis(data_dict,MixtureGaussian, steps=200, lr=0.05) +``` + + +[Full Documentation](https://annealpyro.readthedocs.io/en/latest/) + + + + +%package -n python3-congas +Summary: Copy Number genotyping from single cell RNA sequencing +Provides: python-congas +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-congas +# Copy number genotyping from scRNA sequencing + + +[](https://travis-ci.org/Militeee/congas) +[](https://codecov.io/gh/Militeee/congas) + + +A set of Pyro models and functions to infer CNA from scRNA-seq data. +It comes with a companion R package (hlink) that works as an interface and provides preprocessing, simulation and visualization routines. + + +Currently providing: + +- A mixture model on segments where CNV are modelled as LogNormal random variable (MixtureGaussian) +- Same as above but the number of cluster is learned (MixtureGaussianDMP) +- A model where CNVs are modelled as outcome from Categorical distributions, clusters share the same parameters (MixtureDirichlet) +- A simple Hmm where CNVs are again categorical, but there is no clustering (SimpleHmm) +- The version of MixtureDirichlet but with temporal dependency (HmmMixtureRNA) + +Coming soon: +- A linear model in the emission that can account for known covariates +- The equivalent of MixtureGaussian but with CNVs as Categorical random variable +- A model on genes (all the other models assume a division in segments) + +To install: + +`$ pip install congas` + +To run a simple analysis on the example data + +```python +import congas as cn +from congas.models import MixtureGaussian +data_dict = cn.simulation_data +params, loss = cn.run_analysis(data_dict,MixtureGaussian, steps=200, lr=0.05) +``` + + +[Full Documentation](https://annealpyro.readthedocs.io/en/latest/) + + + + +%package help +Summary: Development documents and examples for congas +Provides: python3-congas-doc +%description help +# Copy number genotyping from scRNA sequencing + + +[](https://travis-ci.org/Militeee/congas) +[](https://codecov.io/gh/Militeee/congas) + + +A set of Pyro models and functions to infer CNA from scRNA-seq data. +It comes with a companion R package (hlink) that works as an interface and provides preprocessing, simulation and visualization routines. + + +Currently providing: + +- A mixture model on segments where CNV are modelled as LogNormal random variable (MixtureGaussian) +- Same as above but the number of cluster is learned (MixtureGaussianDMP) +- A model where CNVs are modelled as outcome from Categorical distributions, clusters share the same parameters (MixtureDirichlet) +- A simple Hmm where CNVs are again categorical, but there is no clustering (SimpleHmm) +- The version of MixtureDirichlet but with temporal dependency (HmmMixtureRNA) + +Coming soon: +- A linear model in the emission that can account for known covariates +- The equivalent of MixtureGaussian but with CNVs as Categorical random variable +- A model on genes (all the other models assume a division in segments) + +To install: + +`$ pip install congas` + +To run a simple analysis on the example data + +```python +import congas as cn +from congas.models import MixtureGaussian +data_dict = cn.simulation_data +params, loss = cn.run_analysis(data_dict,MixtureGaussian, steps=200, lr=0.05) +``` + + +[Full Documentation](https://annealpyro.readthedocs.io/en/latest/) + + + + +%prep +%autosetup -n congas-0.0.75 + +%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-congas -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.0.75-1 +- Package Spec generated @@ -0,0 +1 @@ +106c7e4d0cd356aabda9b331fce878b9 congas-0.0.75.tar.gz |
