Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127

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Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
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@haoqichen20haoqichen20 commented Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)

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@canergencanergen reopened this Nov 13, 2024
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flying-sheep commented Nov 18, 2024•
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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.

So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.

Also there are a few other problems indicated by the checks failing. Please fix.

  • docs:

    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree

  • JSON schema:

    Schema validation errors were encountered.
    tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']

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@haoqichen20@flying-sheep@canergen
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n 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;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127
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Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
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@haoqichen20haoqichen20
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Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)
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@canergencanergen
reopened this
Nov 13, 2024
@flying-sheep
flying-sheep
commented
Nov 18, 2024•

edited

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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.
So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.
Also there are a few other problems indicated by the checks failing. Please fix.
  • docs:
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
…/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree
  • JSON schema:
    Schema validation errors were encountered.
    
tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127
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Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
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@haoqichen20haoqichen20
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Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)
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@canergencanergen
reopened this
Nov 13, 2024
@flying-sheep
flying-sheep
commented
Nov 18, 2024•

edited

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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.
So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.
Also there are a few other problems indicated by the checks failing. Please fix.
  • docs:
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
…/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree
  • JSON schema:
    Schema validation errors were encountered.
    
tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']
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3 participants

@haoqichen20@flying-sheep@canergen

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127
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haoqichen20 wants to merge 5 commits into
scverse:mainfrom 
haoqichen20:pseudobulk_DEA_hack2023
Open
Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
haoqichen20 wants to merge 5 commits into
scverse:mainfrom 
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@haoqichen20haoqichen20
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Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)
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@canergencanergen
reopened this
Nov 13, 2024
@flying-sheep
flying-sheep
commented
Nov 18, 2024•

edited

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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.
So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.
Also there are a few other problems indicated by the checks failing. Please fix.
  • docs:
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
…/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree
  • JSON schema:
    Schema validation errors were encountered.
    
tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']
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3 participants

@haoqichen20@flying-sheep@canergen

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127
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haoqichen20 wants to merge 5 commits into
scverse:mainfrom 
haoqichen20:pseudobulk_DEA_hack2023
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Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
haoqichen20 wants to merge 5 commits into
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@haoqichen20
@haoqichen20haoqichen20
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Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)
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@canergencanergen
reopened this
Nov 13, 2024
@flying-sheep
flying-sheep
commented
Nov 18, 2024•

edited

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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.
So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.
Also there are a few other problems indicated by the checks failing. Please fix.
  • docs:
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
…/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree
  • JSON schema:
    Schema validation errors were encountered.
    
tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']
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3 participants

@haoqichen20@flying-sheep@canergen

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127
Open
haoqichen20 wants to merge 5 commits into
scverse:mainfrom 
haoqichen20:pseudobulk_DEA_hack2023
Open
Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
haoqichen20 wants to merge 5 commits into
scverse:mainfrom 
haoqichen20:pseudobulk_DEA_hack2023
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@haoqichen20
@haoqichen20haoqichen20
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Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)
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reopened this
Nov 13, 2024
@flying-sheep
flying-sheep
commented
Nov 18, 2024•

edited

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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.
So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.
Also there are a few other problems indicated by the checks failing. Please fix.
  • docs:
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
…/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree
  • JSON schema:
    Schema validation errors were encountered.
    
tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']
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3 participants

@haoqichen20@flying-sheep@canergen

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127
Open
haoqichen20 wants to merge 5 commits into
scverse:mainfrom 
haoqichen20:pseudobulk_DEA_hack2023
Open
Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
haoqichen20 wants to merge 5 commits into
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@haoqichen20
@haoqichen20haoqichen20
commented
Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)
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reopened this
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@flying-sheep
flying-sheep
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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.
So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.
Also there are a few other problems indicated by the checks failing. Please fix.
  • docs:
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
…/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree
  • JSON schema:
    Schema validation errors were encountered.
    
tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
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} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
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Add jupyter notebook for pseudobulk_DEA, add support dataset, update … - #127
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Add jupyter notebook for pseudobulk_DEA, add support dataset, update …#127
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@haoqichen20
@haoqichen20haoqichen20
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Nov 29, 2023

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)
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Nov 13, 2024
@flying-sheep
flying-sheep
commented
Nov 18, 2024•

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Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.
So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.
Also there are a few other problems indicated by the checks failing. Please fix.
  • docs:
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
…/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    
checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree
  • JSON schema:
    Schema validation errors were encountered.
    
tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']
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3 participants

@haoqichen20@flying-sheep@canergen