diff options
| author | CoprDistGit <infra@openeuler.org> | 2023-05-31 05:00:51 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-31 05:00:51 +0000 |
| commit | 3199cf4da1fa91e75c5b73645613c044c77e865f (patch) | |
| tree | fdd9ec19fa0f0a89c6e4c988353574188e96e5ac | |
| parent | eabae2f759ab299b13ccc7f2d9732aeaca3784c8 (diff) | |
automatic import of python-flowkit
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-flowkit.spec | 561 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 563 insertions, 0 deletions
@@ -0,0 +1 @@ +/FlowKit-1.0.1.tar.gz diff --git a/python-flowkit.spec b/python-flowkit.spec new file mode 100644 index 0000000..d149b68 --- /dev/null +++ b/python-flowkit.spec @@ -0,0 +1,561 @@ +%global _empty_manifest_terminate_build 0 +Name: python-FlowKit +Version: 1.0.1 +Release: 1 +Summary: Flow Cytometry Toolkit +License: BSD +URL: https://github.com/whitews/flowkit +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/eb/26/65a22954c5ae4bbbb4fe350a6b3e9a7f1149b833c83f1f9593f9f2229f6a/FlowKit-1.0.1.tar.gz +BuildArch: noarch + + +%description +# FlowKit + +[](https://github.com/whitews/flowkit) + +[](https://pypi.python.org/pypi/flowkit/) +[](https://pypi.python.org/pypi/flowkit/) +[](https://pypi.python.org/pypi/flowkit/) +[](https://zenodo.org/badge/latestdoi/138655889) + + +[](https://github.com/whitews/FlowKit/actions/workflows/tests_master.yml) +[](https://github.com/whitews/FlowKit/actions/workflows/tests_develop.yml) +[](https://codecov.io/gh/whitews/flowkit) +[](https://flowkit.readthedocs.io/en/latest/?badge=latest) + +* [Overview](#overview) +* [Features](#features) +* [Requirements](#requirements) +* [Installation](#installation) +* [Documentation](#documentation) + * [Tutorials](#tutorials) + * [Advanced Examples](#advanced-examples) +* [Contributing](#contributing) +* [Cite FlowKit](#cite-flowkit) +* [Projects & Research Using FlowKit](#projects--research-using-flowkit) + +## Overview + +FlowKit is a Python toolkit for flow cytometry analysis and visualization, with full support for the [GatingML 2.0 standard](http://flowcyt.sourceforge.net/gating/latest.pdf) and limited support for FlowJo 10 workspace files. + +<img alt="FlowKit Overview" src="https://raw.githubusercontent.com/whitews/FlowKit/master/docs/_static/flowkit_overview.jpg" style="width:400px;" /> + +## Features + +* Read / Write FCS Files + * Read FCS files, supporting FCS versions 2.0, 3.0, and 3.1 + * Export FCS data as: + * A new FCS 3.1 file + * NumPy array + * Pandas DataFrame + * CSV text file +* Compensation + * Compensate events using spillover matrices from: + * $SPILL or $SPILLOVER keyword value + * FlowJo tab-delimited text + * NumPy array + * GatingML 2.0 spectrumMatrix XML element +* Transformation + * Logicle + * Inverse hyperbolic sine (ArcSinh) + * FlowJo Bi-exponential + * Hyperlog + * Logarithmic + * Channel ratios + * Linear +* Gating + * Full support for the GatingML 2.0 specification + * Import GatingML XML documents as gating strategies + * Export gating strategies as a valid GatingML XML document + * Import FlowJo 10 workspace files, supporting the following features: + * Linear, logarithmic, bi-exponential, and logicle transforms + * Polygon, rectangle, ellipse, and quadrant gates + * Programmatically create gating strategies including polygon, rectangle, range, ellipsoid, quadrant, and boolean gates + * Retrieve gating results as a Pandas DataFrame +* Visualization + * Histogram of single channel data + * Contour density plot of two channels + * Interactive scatter plot of two channels + * Interactive scatter plot matrix of any combination of channels + * Interactive scatter plots of gates with sample events + +## Requirements + +FlowKit supports Python version 3.7 - 3.10. All dependencies are installable +via pip, and are listed below. + +> **NOTE**: FlowUtils uses C extensions for significant performance improvements. For most platforms and Python versions, pre-built binaries are available in PyPI (i.e. installable via `pip`). +> +> If a pre-built binary of FlowUtils is not available for your environment, the C extensions must be compiled using the source package. NumPy >=1.19 must be installed prior to compiling FlowUtils. If compiling using `gcc`, version 5 or later is required. + +Required Python dependencies: + +* [flowio](https://github.com/whitews/flowio) == 1.1.1 +* [flowutils](https://github.com/whitews/flowutils) == 1.0.0 +* anytree >= 2.6 +* bokeh >= 2.4, <3.0 +* lxml >= 4.7 +* matplotlib >= 3.5 +* networkx >= 2.3 +* numpy >= 1.20 +* pandas >= 1.2 +* psutils >= 5.8 +* scipy >= 1.6 +* seaborn >= 0.11, <0.12 + +## Installation + +> **NOTE**: For macOS users running on Apple Silicon, the version of `pip` may need to be upgraded prior to installing FlowKit in order to install the required dependencies. + +### From PyPI + +``` +pip install flowkit +``` + +### From source + +Clone the repository and ensure `pip` is up-to-date. It is recommended to use `pip` to install requirements as relying on `setuptools` may result in incompatible dependency versions. + +``` +git clone https://github.com/whitews/flowkit +cd flowkit +pip install --upgrade pip +pip install -r requirements.txt +python setup.py install +``` + +## Documentation + +The FlowKit API documentation is available [on ReadTheDocs here](https://flowkit.readthedocs.io/en/latest/?badge=latest). The tutorial notebooks in the `docs/notebooks` directory are a great place to get started with FlowKit, and are linked below. +If you have any questions about FlowKit, find any bugs, or feel something is missing from the tutorials below [please submit an issue to the GitHub repository here](https://github.com/whitews/FlowKit/issues/new/). + +### Changelogs + +[Changelogs for versions are available here](https://github.com/whitews/FlowKit/releases) + +### Tutorials + +The series of Jupyter notebook tutorials can be found in the `docs/notebooks` directory of this repository. Note, the interactive scatterplots do not render on GitHub. The rendered versions are available on our [documentation page here](https://flowkit.readthedocs.io/en/latest/?badge=latest). Or, clone the repo and run them locally to see the fully interactive plots. + +* [Part 1 - Sample Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part01-sample-class.ipynb) +* [Part 2 - transforms Module & Matrix Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part02-transforms-module-matrix-class.ipynb) +* [Part 3 - GatingStrategy & GatingResults Classes](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part03-gating-strategy-and-gating-results-classes.ipynb) +* [Part 4 - gates Module](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part04-gates-module.ipynb) +* [Part 5 - Session Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part05-session-class.ipynb) +* [Part 6 - Workspace Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part06-workspace-class.ipynb) + +### Advanced Examples + +Below are more advanced and practical examples for using FlowKit. If you have an example you would like to submit for consideration in this list (preferably with data), please [submit an issue](https://github.com/whitews/FlowKit/issues/new/). + +* [Compare mean fluorescence intensity (MFI) in gated populations](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/flowkit-session-compare-mfi-of-gated-events.ipynb) +* [Importing a FlowJo 10 WSP file & replicating analysis in FlowKit](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/flowkit-session-replicate-flowjo-wsp.ipynb) +* [Dimension reduction on gated populations](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/dimension_reduction_on_gated_populations.ipynb) +* [Comparison between Leiden & Louvain clustering](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/clustering_comparison_leiden_vs_louvain.ipynb) +* [Saving Flow Analysis Data as AnnData objects for ScanPy](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/scanpy_creating_and_using_AnnData_objects.ipynb) + +## Contributing + +Want to get involved in the development of FlowKit? + +[Read our CONTRIBUTING guidelines](https://github.com/whitews/FlowKit/blob/master/CONTRIBUTING.md) + +## Cite FlowKit + +[White, S., Quinn, J., Enzor, J., Staats, J., Mosier, S. M., Almarode, J., Denny, T. N., Weinhold, K. J., Ferrari, G., & Chan, C. (2021). FlowKit: A Python toolkit for integrated manual and automated cytometry analysis workflows. Frontiers in Immunology, 12. https://doi.org/10.3389/fimmu.2021.768541](https://www.frontiersin.org/articles/10.3389/fimmu.2021.768541/full) + +## Projects & Research Using FlowKit + +The following projects and publications have utilized FlowKit. If you have a package or publication where FlowKit was used, and you want it listed here, feel free to [submit an issue](https://github.com/whitews/FlowKit/issues/new/) letting me know. + +* Schuster, Jonas et al. “Combining real-time fluorescence spectroscopy and flow cytometry to reveal new insights in DOC and cell characterization of drinking water.” Frontiers in Environmental Chemistry (2022), [doi:10.3389/fenvc.2022.931067](https://www.frontiersin.org/articles/10.3389/fenvc.2022.931067/full) +* Rendeiro, André F et al. "Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression." Life science alliance vol. 4,2 e202000955. 24 Dec. 2020, [doi:10.26508/lsa.202000955](https://www.life-science-alliance.org/content/4/2/e202000955.full) + + +%package -n python3-FlowKit +Summary: Flow Cytometry Toolkit +Provides: python-FlowKit +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-FlowKit +# FlowKit + +[](https://github.com/whitews/flowkit) + +[](https://pypi.python.org/pypi/flowkit/) +[](https://pypi.python.org/pypi/flowkit/) +[](https://pypi.python.org/pypi/flowkit/) +[](https://zenodo.org/badge/latestdoi/138655889) + + +[](https://github.com/whitews/FlowKit/actions/workflows/tests_master.yml) +[](https://github.com/whitews/FlowKit/actions/workflows/tests_develop.yml) +[](https://codecov.io/gh/whitews/flowkit) +[](https://flowkit.readthedocs.io/en/latest/?badge=latest) + +* [Overview](#overview) +* [Features](#features) +* [Requirements](#requirements) +* [Installation](#installation) +* [Documentation](#documentation) + * [Tutorials](#tutorials) + * [Advanced Examples](#advanced-examples) +* [Contributing](#contributing) +* [Cite FlowKit](#cite-flowkit) +* [Projects & Research Using FlowKit](#projects--research-using-flowkit) + +## Overview + +FlowKit is a Python toolkit for flow cytometry analysis and visualization, with full support for the [GatingML 2.0 standard](http://flowcyt.sourceforge.net/gating/latest.pdf) and limited support for FlowJo 10 workspace files. + +<img alt="FlowKit Overview" src="https://raw.githubusercontent.com/whitews/FlowKit/master/docs/_static/flowkit_overview.jpg" style="width:400px;" /> + +## Features + +* Read / Write FCS Files + * Read FCS files, supporting FCS versions 2.0, 3.0, and 3.1 + * Export FCS data as: + * A new FCS 3.1 file + * NumPy array + * Pandas DataFrame + * CSV text file +* Compensation + * Compensate events using spillover matrices from: + * $SPILL or $SPILLOVER keyword value + * FlowJo tab-delimited text + * NumPy array + * GatingML 2.0 spectrumMatrix XML element +* Transformation + * Logicle + * Inverse hyperbolic sine (ArcSinh) + * FlowJo Bi-exponential + * Hyperlog + * Logarithmic + * Channel ratios + * Linear +* Gating + * Full support for the GatingML 2.0 specification + * Import GatingML XML documents as gating strategies + * Export gating strategies as a valid GatingML XML document + * Import FlowJo 10 workspace files, supporting the following features: + * Linear, logarithmic, bi-exponential, and logicle transforms + * Polygon, rectangle, ellipse, and quadrant gates + * Programmatically create gating strategies including polygon, rectangle, range, ellipsoid, quadrant, and boolean gates + * Retrieve gating results as a Pandas DataFrame +* Visualization + * Histogram of single channel data + * Contour density plot of two channels + * Interactive scatter plot of two channels + * Interactive scatter plot matrix of any combination of channels + * Interactive scatter plots of gates with sample events + +## Requirements + +FlowKit supports Python version 3.7 - 3.10. All dependencies are installable +via pip, and are listed below. + +> **NOTE**: FlowUtils uses C extensions for significant performance improvements. For most platforms and Python versions, pre-built binaries are available in PyPI (i.e. installable via `pip`). +> +> If a pre-built binary of FlowUtils is not available for your environment, the C extensions must be compiled using the source package. NumPy >=1.19 must be installed prior to compiling FlowUtils. If compiling using `gcc`, version 5 or later is required. + +Required Python dependencies: + +* [flowio](https://github.com/whitews/flowio) == 1.1.1 +* [flowutils](https://github.com/whitews/flowutils) == 1.0.0 +* anytree >= 2.6 +* bokeh >= 2.4, <3.0 +* lxml >= 4.7 +* matplotlib >= 3.5 +* networkx >= 2.3 +* numpy >= 1.20 +* pandas >= 1.2 +* psutils >= 5.8 +* scipy >= 1.6 +* seaborn >= 0.11, <0.12 + +## Installation + +> **NOTE**: For macOS users running on Apple Silicon, the version of `pip` may need to be upgraded prior to installing FlowKit in order to install the required dependencies. + +### From PyPI + +``` +pip install flowkit +``` + +### From source + +Clone the repository and ensure `pip` is up-to-date. It is recommended to use `pip` to install requirements as relying on `setuptools` may result in incompatible dependency versions. + +``` +git clone https://github.com/whitews/flowkit +cd flowkit +pip install --upgrade pip +pip install -r requirements.txt +python setup.py install +``` + +## Documentation + +The FlowKit API documentation is available [on ReadTheDocs here](https://flowkit.readthedocs.io/en/latest/?badge=latest). The tutorial notebooks in the `docs/notebooks` directory are a great place to get started with FlowKit, and are linked below. +If you have any questions about FlowKit, find any bugs, or feel something is missing from the tutorials below [please submit an issue to the GitHub repository here](https://github.com/whitews/FlowKit/issues/new/). + +### Changelogs + +[Changelogs for versions are available here](https://github.com/whitews/FlowKit/releases) + +### Tutorials + +The series of Jupyter notebook tutorials can be found in the `docs/notebooks` directory of this repository. Note, the interactive scatterplots do not render on GitHub. The rendered versions are available on our [documentation page here](https://flowkit.readthedocs.io/en/latest/?badge=latest). Or, clone the repo and run them locally to see the fully interactive plots. + +* [Part 1 - Sample Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part01-sample-class.ipynb) +* [Part 2 - transforms Module & Matrix Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part02-transforms-module-matrix-class.ipynb) +* [Part 3 - GatingStrategy & GatingResults Classes](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part03-gating-strategy-and-gating-results-classes.ipynb) +* [Part 4 - gates Module](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part04-gates-module.ipynb) +* [Part 5 - Session Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part05-session-class.ipynb) +* [Part 6 - Workspace Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part06-workspace-class.ipynb) + +### Advanced Examples + +Below are more advanced and practical examples for using FlowKit. If you have an example you would like to submit for consideration in this list (preferably with data), please [submit an issue](https://github.com/whitews/FlowKit/issues/new/). + +* [Compare mean fluorescence intensity (MFI) in gated populations](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/flowkit-session-compare-mfi-of-gated-events.ipynb) +* [Importing a FlowJo 10 WSP file & replicating analysis in FlowKit](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/flowkit-session-replicate-flowjo-wsp.ipynb) +* [Dimension reduction on gated populations](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/dimension_reduction_on_gated_populations.ipynb) +* [Comparison between Leiden & Louvain clustering](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/clustering_comparison_leiden_vs_louvain.ipynb) +* [Saving Flow Analysis Data as AnnData objects for ScanPy](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/scanpy_creating_and_using_AnnData_objects.ipynb) + +## Contributing + +Want to get involved in the development of FlowKit? + +[Read our CONTRIBUTING guidelines](https://github.com/whitews/FlowKit/blob/master/CONTRIBUTING.md) + +## Cite FlowKit + +[White, S., Quinn, J., Enzor, J., Staats, J., Mosier, S. M., Almarode, J., Denny, T. N., Weinhold, K. J., Ferrari, G., & Chan, C. (2021). FlowKit: A Python toolkit for integrated manual and automated cytometry analysis workflows. Frontiers in Immunology, 12. https://doi.org/10.3389/fimmu.2021.768541](https://www.frontiersin.org/articles/10.3389/fimmu.2021.768541/full) + +## Projects & Research Using FlowKit + +The following projects and publications have utilized FlowKit. If you have a package or publication where FlowKit was used, and you want it listed here, feel free to [submit an issue](https://github.com/whitews/FlowKit/issues/new/) letting me know. + +* Schuster, Jonas et al. “Combining real-time fluorescence spectroscopy and flow cytometry to reveal new insights in DOC and cell characterization of drinking water.” Frontiers in Environmental Chemistry (2022), [doi:10.3389/fenvc.2022.931067](https://www.frontiersin.org/articles/10.3389/fenvc.2022.931067/full) +* Rendeiro, André F et al. "Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression." Life science alliance vol. 4,2 e202000955. 24 Dec. 2020, [doi:10.26508/lsa.202000955](https://www.life-science-alliance.org/content/4/2/e202000955.full) + + +%package help +Summary: Development documents and examples for FlowKit +Provides: python3-FlowKit-doc +%description help +# FlowKit + +[](https://github.com/whitews/flowkit) + +[](https://pypi.python.org/pypi/flowkit/) +[](https://pypi.python.org/pypi/flowkit/) +[](https://pypi.python.org/pypi/flowkit/) +[](https://zenodo.org/badge/latestdoi/138655889) + + +[](https://github.com/whitews/FlowKit/actions/workflows/tests_master.yml) +[](https://github.com/whitews/FlowKit/actions/workflows/tests_develop.yml) +[](https://codecov.io/gh/whitews/flowkit) +[](https://flowkit.readthedocs.io/en/latest/?badge=latest) + +* [Overview](#overview) +* [Features](#features) +* [Requirements](#requirements) +* [Installation](#installation) +* [Documentation](#documentation) + * [Tutorials](#tutorials) + * [Advanced Examples](#advanced-examples) +* [Contributing](#contributing) +* [Cite FlowKit](#cite-flowkit) +* [Projects & Research Using FlowKit](#projects--research-using-flowkit) + +## Overview + +FlowKit is a Python toolkit for flow cytometry analysis and visualization, with full support for the [GatingML 2.0 standard](http://flowcyt.sourceforge.net/gating/latest.pdf) and limited support for FlowJo 10 workspace files. + +<img alt="FlowKit Overview" src="https://raw.githubusercontent.com/whitews/FlowKit/master/docs/_static/flowkit_overview.jpg" style="width:400px;" /> + +## Features + +* Read / Write FCS Files + * Read FCS files, supporting FCS versions 2.0, 3.0, and 3.1 + * Export FCS data as: + * A new FCS 3.1 file + * NumPy array + * Pandas DataFrame + * CSV text file +* Compensation + * Compensate events using spillover matrices from: + * $SPILL or $SPILLOVER keyword value + * FlowJo tab-delimited text + * NumPy array + * GatingML 2.0 spectrumMatrix XML element +* Transformation + * Logicle + * Inverse hyperbolic sine (ArcSinh) + * FlowJo Bi-exponential + * Hyperlog + * Logarithmic + * Channel ratios + * Linear +* Gating + * Full support for the GatingML 2.0 specification + * Import GatingML XML documents as gating strategies + * Export gating strategies as a valid GatingML XML document + * Import FlowJo 10 workspace files, supporting the following features: + * Linear, logarithmic, bi-exponential, and logicle transforms + * Polygon, rectangle, ellipse, and quadrant gates + * Programmatically create gating strategies including polygon, rectangle, range, ellipsoid, quadrant, and boolean gates + * Retrieve gating results as a Pandas DataFrame +* Visualization + * Histogram of single channel data + * Contour density plot of two channels + * Interactive scatter plot of two channels + * Interactive scatter plot matrix of any combination of channels + * Interactive scatter plots of gates with sample events + +## Requirements + +FlowKit supports Python version 3.7 - 3.10. All dependencies are installable +via pip, and are listed below. + +> **NOTE**: FlowUtils uses C extensions for significant performance improvements. For most platforms and Python versions, pre-built binaries are available in PyPI (i.e. installable via `pip`). +> +> If a pre-built binary of FlowUtils is not available for your environment, the C extensions must be compiled using the source package. NumPy >=1.19 must be installed prior to compiling FlowUtils. If compiling using `gcc`, version 5 or later is required. + +Required Python dependencies: + +* [flowio](https://github.com/whitews/flowio) == 1.1.1 +* [flowutils](https://github.com/whitews/flowutils) == 1.0.0 +* anytree >= 2.6 +* bokeh >= 2.4, <3.0 +* lxml >= 4.7 +* matplotlib >= 3.5 +* networkx >= 2.3 +* numpy >= 1.20 +* pandas >= 1.2 +* psutils >= 5.8 +* scipy >= 1.6 +* seaborn >= 0.11, <0.12 + +## Installation + +> **NOTE**: For macOS users running on Apple Silicon, the version of `pip` may need to be upgraded prior to installing FlowKit in order to install the required dependencies. + +### From PyPI + +``` +pip install flowkit +``` + +### From source + +Clone the repository and ensure `pip` is up-to-date. It is recommended to use `pip` to install requirements as relying on `setuptools` may result in incompatible dependency versions. + +``` +git clone https://github.com/whitews/flowkit +cd flowkit +pip install --upgrade pip +pip install -r requirements.txt +python setup.py install +``` + +## Documentation + +The FlowKit API documentation is available [on ReadTheDocs here](https://flowkit.readthedocs.io/en/latest/?badge=latest). The tutorial notebooks in the `docs/notebooks` directory are a great place to get started with FlowKit, and are linked below. +If you have any questions about FlowKit, find any bugs, or feel something is missing from the tutorials below [please submit an issue to the GitHub repository here](https://github.com/whitews/FlowKit/issues/new/). + +### Changelogs + +[Changelogs for versions are available here](https://github.com/whitews/FlowKit/releases) + +### Tutorials + +The series of Jupyter notebook tutorials can be found in the `docs/notebooks` directory of this repository. Note, the interactive scatterplots do not render on GitHub. The rendered versions are available on our [documentation page here](https://flowkit.readthedocs.io/en/latest/?badge=latest). Or, clone the repo and run them locally to see the fully interactive plots. + +* [Part 1 - Sample Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part01-sample-class.ipynb) +* [Part 2 - transforms Module & Matrix Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part02-transforms-module-matrix-class.ipynb) +* [Part 3 - GatingStrategy & GatingResults Classes](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part03-gating-strategy-and-gating-results-classes.ipynb) +* [Part 4 - gates Module](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part04-gates-module.ipynb) +* [Part 5 - Session Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part05-session-class.ipynb) +* [Part 6 - Workspace Class](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/flowkit-tutorial-part06-workspace-class.ipynb) + +### Advanced Examples + +Below are more advanced and practical examples for using FlowKit. If you have an example you would like to submit for consideration in this list (preferably with data), please [submit an issue](https://github.com/whitews/FlowKit/issues/new/). + +* [Compare mean fluorescence intensity (MFI) in gated populations](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/flowkit-session-compare-mfi-of-gated-events.ipynb) +* [Importing a FlowJo 10 WSP file & replicating analysis in FlowKit](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/flowkit-session-replicate-flowjo-wsp.ipynb) +* [Dimension reduction on gated populations](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/dimension_reduction_on_gated_populations.ipynb) +* [Comparison between Leiden & Louvain clustering](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/clustering_comparison_leiden_vs_louvain.ipynb) +* [Saving Flow Analysis Data as AnnData objects for ScanPy](https://github.com/whitews/FlowKit/blob/master/docs/notebooks/advanced/scanpy_creating_and_using_AnnData_objects.ipynb) + +## Contributing + +Want to get involved in the development of FlowKit? + +[Read our CONTRIBUTING guidelines](https://github.com/whitews/FlowKit/blob/master/CONTRIBUTING.md) + +## Cite FlowKit + +[White, S., Quinn, J., Enzor, J., Staats, J., Mosier, S. M., Almarode, J., Denny, T. N., Weinhold, K. J., Ferrari, G., & Chan, C. (2021). FlowKit: A Python toolkit for integrated manual and automated cytometry analysis workflows. Frontiers in Immunology, 12. https://doi.org/10.3389/fimmu.2021.768541](https://www.frontiersin.org/articles/10.3389/fimmu.2021.768541/full) + +## Projects & Research Using FlowKit + +The following projects and publications have utilized FlowKit. If you have a package or publication where FlowKit was used, and you want it listed here, feel free to [submit an issue](https://github.com/whitews/FlowKit/issues/new/) letting me know. + +* Schuster, Jonas et al. “Combining real-time fluorescence spectroscopy and flow cytometry to reveal new insights in DOC and cell characterization of drinking water.” Frontiers in Environmental Chemistry (2022), [doi:10.3389/fenvc.2022.931067](https://www.frontiersin.org/articles/10.3389/fenvc.2022.931067/full) +* Rendeiro, André F et al. "Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression." Life science alliance vol. 4,2 e202000955. 24 Dec. 2020, [doi:10.26508/lsa.202000955](https://www.life-science-alliance.org/content/4/2/e202000955.full) + + +%prep +%autosetup -n FlowKit-1.0.1 + +%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-FlowKit -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 1.0.1-1 +- Package Spec generated @@ -0,0 +1 @@ +b6cdfc2a1a3997d2c3509ed409bac257 FlowKit-1.0.1.tar.gz |