Skip to content
BranchesTags

Repository files navigation

patpy – sample-level analysis framework for single-cell data

patpy is a toolbox for single-cell data analysis on sample level.

It provides:

  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation

overview

⚠️ Warning: Development in Progress ⚠️

This repository is currently under active development Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.

Please proceed with caution and feel free to contribute, but be aware that:

  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.

If you have any questions or face bugs, feel free to open an issue.

Thank you for your patience and interest. Stay tuned for updates!

TestsCoveragePyPIDocumentation

Getting started

Please refer to the documentation. In particular, the

Installation

You need to have Python 3.9 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

There are several alternative options to install patpy:

  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main

To install specific dependencies for some sample representation tools, use the following command:

pip install patpy[pilot]

All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.

Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:

# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Building docs

  1. Install sphinx

You may need add path to sphinx-doc to the $PATH

  1. Install other doc section dependencies from the pyproject.toml

  2. Build the documentation pages:

cd docs
make html
  1. Open docs/_build/html/index.html

Citation

Preprint is coming soon. So far, you can refer to this repository as following:

APA

Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/

BibTeX

@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}

About

Toolbox for single-cell data analysis on sample level

Resources

Readme
License

Contributing

Contributing
Activity

Stars

0 stars

Watchers

0 watching

Forks

0 forks
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
GitHub - schrf/patpy: Toolbox for single-cell data analysis on sample level · GitHub
Skip to content
BranchesTags
Repository files navigation
patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation
overview
⚠️ Warning: Development in Progress ⚠️
This repository is currently under active development
Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
Please proceed with caution and feel free to contribute, but be aware that:
  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an issue.
Thank you for your patience and interest. Stay tuned for updates!
TestsCoveragePyPIDocumentation
Getting started
Please refer to the documentation. In particular, the
Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing Mambaforge.
There are several alternative options to install patpy:
  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main
To install specific dependencies for some sample representation tools, use the following command:
pip install patpy[pilot]
All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.
Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:
# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse.
If you found a bug, please use the issue tracker.
Building docs
  1. Install sphinx
You may need add path to sphinx-doc to the $PATH
  1. Install other doc section dependencies from the pyproject.toml
  2. Build the documentation pages:
cd docs
make html
  1. Open docs/_build/html/index.html
Citation
Preprint is coming soon. So far, you can refer to this repository as following:
APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
BibTeX
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}
About
Toolbox for single-cell data analysis on sample level
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - schrf/patpy: Toolbox for single-cell data analysis on sample level · GitHub
Skip to content
BranchesTags
Repository files navigation
patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation
overview
⚠️ Warning: Development in Progress ⚠️
This repository is currently under active development
Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
Please proceed with caution and feel free to contribute, but be aware that:
  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an issue.
Thank you for your patience and interest. Stay tuned for updates!
TestsCoveragePyPIDocumentation
Getting started
Please refer to the documentation. In particular, the
Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing Mambaforge.
There are several alternative options to install patpy:
  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main
To install specific dependencies for some sample representation tools, use the following command:
pip install patpy[pilot]
All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.
Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:
# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse.
If you found a bug, please use the issue tracker.
Building docs
  1. Install sphinx
You may need add path to sphinx-doc to the $PATH
  1. Install other doc section dependencies from the pyproject.toml
  2. Build the documentation pages:
cd docs
make html
  1. Open docs/_build/html/index.html
Citation
Preprint is coming soon. So far, you can refer to this repository as following:
APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
BibTeX
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}
About
Toolbox for single-cell data analysis on sample level
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - schrf/patpy: Toolbox for single-cell data analysis on sample level · GitHub
Skip to content
BranchesTags
Repository files navigation
patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation
overview
⚠️ Warning: Development in Progress ⚠️
This repository is currently under active development
Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
Please proceed with caution and feel free to contribute, but be aware that:
  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an issue.
Thank you for your patience and interest. Stay tuned for updates!
TestsCoveragePyPIDocumentation
Getting started
Please refer to the documentation. In particular, the
Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing Mambaforge.
There are several alternative options to install patpy:
  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main
To install specific dependencies for some sample representation tools, use the following command:
pip install patpy[pilot]
All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.
Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:
# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse.
If you found a bug, please use the issue tracker.
Building docs
  1. Install sphinx
You may need add path to sphinx-doc to the $PATH
  1. Install other doc section dependencies from the pyproject.toml
  2. Build the documentation pages:
cd docs
make html
  1. Open docs/_build/html/index.html
Citation
Preprint is coming soon. So far, you can refer to this repository as following:
APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
BibTeX
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}
About
Toolbox for single-cell data analysis on sample level
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - schrf/patpy: Toolbox for single-cell data analysis on sample level · GitHub
Skip to content
BranchesTags
Repository files navigation
patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation
overview
⚠️ Warning: Development in Progress ⚠️
This repository is currently under active development
Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
Please proceed with caution and feel free to contribute, but be aware that:
  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an issue.
Thank you for your patience and interest. Stay tuned for updates!
TestsCoveragePyPIDocumentation
Getting started
Please refer to the documentation. In particular, the
Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing Mambaforge.
There are several alternative options to install patpy:
  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main
To install specific dependencies for some sample representation tools, use the following command:
pip install patpy[pilot]
All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.
Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:
# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse.
If you found a bug, please use the issue tracker.
Building docs
  1. Install sphinx
You may need add path to sphinx-doc to the $PATH
  1. Install other doc section dependencies from the pyproject.toml
  2. Build the documentation pages:
cd docs
make html
  1. Open docs/_build/html/index.html
Citation
Preprint is coming soon. So far, you can refer to this repository as following:
APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
BibTeX
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}
About
Toolbox for single-cell data analysis on sample level
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - schrf/patpy: Toolbox for single-cell data analysis on sample level · GitHub
Skip to content
BranchesTags
Repository files navigation
patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation
overview
⚠️ Warning: Development in Progress ⚠️
This repository is currently under active development
Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
Please proceed with caution and feel free to contribute, but be aware that:
  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an issue.
Thank you for your patience and interest. Stay tuned for updates!
TestsCoveragePyPIDocumentation
Getting started
Please refer to the documentation. In particular, the
Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing Mambaforge.
There are several alternative options to install patpy:
  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main
To install specific dependencies for some sample representation tools, use the following command:
pip install patpy[pilot]
All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.
Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:
# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse.
If you found a bug, please use the issue tracker.
Building docs
  1. Install sphinx
You may need add path to sphinx-doc to the $PATH
  1. Install other doc section dependencies from the pyproject.toml
  2. Build the documentation pages:
cd docs
make html
  1. Open docs/_build/html/index.html
Citation
Preprint is coming soon. So far, you can refer to this repository as following:
APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
BibTeX
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}
About
Toolbox for single-cell data analysis on sample level
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - schrf/patpy: Toolbox for single-cell data analysis on sample level · GitHub
Skip to content
BranchesTags
Repository files navigation
patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation
overview
⚠️ Warning: Development in Progress ⚠️
This repository is currently under active development
Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
Please proceed with caution and feel free to contribute, but be aware that:
  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an issue.
Thank you for your patience and interest. Stay tuned for updates!
TestsCoveragePyPIDocumentation
Getting started
Please refer to the documentation. In particular, the
Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing Mambaforge.
There are several alternative options to install patpy:
  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main
To install specific dependencies for some sample representation tools, use the following command:
pip install patpy[pilot]
All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.
Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:
# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse.
If you found a bug, please use the issue tracker.
Building docs
  1. Install sphinx
You may need add path to sphinx-doc to the $PATH
  1. Install other doc section dependencies from the pyproject.toml
  2. Build the documentation pages:
cd docs
make html
  1. Open docs/_build/html/index.html
Citation
Preprint is coming soon. So far, you can refer to this repository as following:
APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
BibTeX
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}
About
Toolbox for single-cell data analysis on sample level
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
GitHub - schrf/patpy: Toolbox for single-cell data analysis on sample level · GitHub
Skip to content
BranchesTags
Repository files navigation
patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
  • 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)
  • 📈 Analysis functions to get the most of your data
  • 📊 Metrics for sample representation evaluation
overview
⚠️ Warning: Development in Progress ⚠️
This repository is currently under active development
Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
Please proceed with caution and feel free to contribute, but be aware that:
  • The codebase is still evolving.
  • Documentation may be incomplete.
  • Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an issue.
Thank you for your patience and interest. Stay tuned for updates!
TestsCoveragePyPIDocumentation
Getting started
Please refer to the documentation. In particular, the
Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing Mambaforge.
There are several alternative options to install patpy:
  1. Install the latest release of patpy from PyPI:
pip install patpy
  1. Install the latest development version:
pip install git+https://github.com/lueckenlab/patpy.git@main
To install specific dependencies for some sample representation tools, use the following command:
pip install patpy[pilot]
All the available dependency groups: diffusionemd, mrvi, pilot, scpoli, wassersteintsne.
Some sample representation tools depend on packages not published on PyPI. To use them, install the extra and the upstream package from git:
# pascient
pip install patpy[pascient]
pip install git+https://github.com/genentech/pascient.git@main
# pulsar
pip install git+https://github.com/snap-stanford/PULSAR.git@main
Release notes
See the changelog.
Contact
For questions and help requests, you can reach out in the scverse discourse.
If you found a bug, please use the issue tracker.
Building docs
  1. Install sphinx
You may need add path to sphinx-doc to the $PATH
  1. Install other doc section dependencies from the pyproject.toml
  2. Build the documentation pages:
cd docs
make html
  1. Open docs/_build/html/index.html
Citation
Preprint is coming soon. So far, you can refer to this repository as following:
APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
BibTeX
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.15.2}
}
About
Toolbox for single-cell data analysis on sample level
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages