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stLearn-tutorials

Tutorials used for stLearn documentation.

Setup

  • Make sure you have git lfs installed and inited as there are some large files in annotations.

Conda Environment

Create

conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:

pip install -e "/path/to/stlearn/directory[jupyter]"

OR

python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running

Witht the stlearn conda enviroment activate run:

process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.

Remove

conda env remove --prefix [some-directory]/conda/stlearn --y

About

Tutorials used for stLearn documentation

Resources

Readme
BSD-3-Clause license
Activity
Custom properties

Stars

0 stars

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0 watching

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0 forks
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, '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 - GenomicsMachineLearning/stLearn-tutorials: Tutorials used for stLearn documentation · GitHub
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56 Commits
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annotations
annotations
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notebooks
.gitattributes
.gitattributes
.gitignore
.gitignore
LICENSE
LICENSE
README.md
README.md
process.sh
process.sh
Repository files navigation
stLearn-tutorials
Tutorials used for stLearn documentation.
Setup
  • Make sure you have git lfs installed and inited as there are some large files in annotations.
Conda Environment
Create
conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:
pip install -e "/path/to/stlearn/directory[jupyter]"

OR
python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running
Witht the stlearn conda enviroment activate run:
process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.
Remove
conda env remove --prefix [some-directory]/conda/stlearn --y

About
Tutorials used for stLearn documentation
Resources
Readme
BSD-3-Clause license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, '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 - GenomicsMachineLearning/stLearn-tutorials: Tutorials used for stLearn documentation · GitHub
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56 Commits
Folders and files
NameName
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annotations
annotations
notebooks
notebooks
.gitattributes
.gitattributes
.gitignore
.gitignore
LICENSE
LICENSE
README.md
README.md
process.sh
process.sh
Repository files navigation
stLearn-tutorials
Tutorials used for stLearn documentation.
Setup
  • Make sure you have git lfs installed and inited as there are some large files in annotations.
Conda Environment
Create
conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:
pip install -e "/path/to/stlearn/directory[jupyter]"

OR
python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running
Witht the stlearn conda enviroment activate run:
process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.
Remove
conda env remove --prefix [some-directory]/conda/stlearn --y

About
Tutorials used for stLearn documentation
Resources
Readme
BSD-3-Clause license
Activity
Custom properties
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 - GenomicsMachineLearning/stLearn-tutorials: Tutorials used for stLearn documentation · GitHub
Skip to content
BranchesTags
Latest commit
History
56 Commits
Folders and files
NameName
Last commit message
Last commit date
annotations
annotations
notebooks
notebooks
.gitattributes
.gitattributes
.gitignore
.gitignore
LICENSE
LICENSE
README.md
README.md
process.sh
process.sh
Repository files navigation
stLearn-tutorials
Tutorials used for stLearn documentation.
Setup
  • Make sure you have git lfs installed and inited as there are some large files in annotations.
Conda Environment
Create
conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:
pip install -e "/path/to/stlearn/directory[jupyter]"

OR
python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running
Witht the stlearn conda enviroment activate run:
process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.
Remove
conda env remove --prefix [some-directory]/conda/stlearn --y

About
Tutorials used for stLearn documentation
Resources
Readme
BSD-3-Clause license
Activity
Custom properties
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 - GenomicsMachineLearning/stLearn-tutorials: Tutorials used for stLearn documentation · GitHub
Skip to content
BranchesTags
Latest commit
History
56 Commits
Folders and files
NameName
Last commit message
Last commit date
annotations
annotations
notebooks
notebooks
.gitattributes
.gitattributes
.gitignore
.gitignore
LICENSE
LICENSE
README.md
README.md
process.sh
process.sh
Repository files navigation
stLearn-tutorials
Tutorials used for stLearn documentation.
Setup
  • Make sure you have git lfs installed and inited as there are some large files in annotations.
Conda Environment
Create
conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:
pip install -e "/path/to/stlearn/directory[jupyter]"

OR
python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running
Witht the stlearn conda enviroment activate run:
process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.
Remove
conda env remove --prefix [some-directory]/conda/stlearn --y

About
Tutorials used for stLearn documentation
Resources
Readme
BSD-3-Clause license
Activity
Custom properties
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 - GenomicsMachineLearning/stLearn-tutorials: Tutorials used for stLearn documentation · GitHub
Skip to content
BranchesTags
Latest commit
History
56 Commits
Folders and files
NameName
Last commit message
Last commit date
annotations
annotations
notebooks
notebooks
.gitattributes
.gitattributes
.gitignore
.gitignore
LICENSE
LICENSE
README.md
README.md
process.sh
process.sh
Repository files navigation
stLearn-tutorials
Tutorials used for stLearn documentation.
Setup
  • Make sure you have git lfs installed and inited as there are some large files in annotations.
Conda Environment
Create
conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:
pip install -e "/path/to/stlearn/directory[jupyter]"

OR
python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running
Witht the stlearn conda enviroment activate run:
process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.
Remove
conda env remove --prefix [some-directory]/conda/stlearn --y

About
Tutorials used for stLearn documentation
Resources
Readme
BSD-3-Clause license
Activity
Custom properties
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); }
})();
})();
GitHub - GenomicsMachineLearning/stLearn-tutorials: Tutorials used for stLearn documentation · GitHub
Skip to content
BranchesTags
Latest commit
History
56 Commits
Folders and files
NameName
Last commit message
Last commit date
annotations
annotations
notebooks
notebooks
.gitattributes
.gitattributes
.gitignore
.gitignore
LICENSE
LICENSE
README.md
README.md
process.sh
process.sh
Repository files navigation
stLearn-tutorials
Tutorials used for stLearn documentation.
Setup
  • Make sure you have git lfs installed and inited as there are some large files in annotations.
Conda Environment
Create
conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:
pip install -e "/path/to/stlearn/directory[jupyter]"

OR
python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running
Witht the stlearn conda enviroment activate run:
process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.
Remove
conda env remove --prefix [some-directory]/conda/stlearn --y

About
Tutorials used for stLearn documentation
Resources
Readme
BSD-3-Clause license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages