BranchesTags

Repository files navigation

scverse tutorials

Documentation

On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be performed with scverse core and ecosystem packages.

To this end, this repository contains:

  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core and ecosystem packages (see docs)

Adding tutorials

If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request in the next open community meeting and potentially suggest improvements.

To be added to our website, tutorials must fulfill at least the following requirements:

  • all featured packages must be scverse core or approved ecosystem packages. This does not apply to packages that are not specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial

You can easily check your changes to tutorials or the registry locally:

hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry

Structure of external tutorials

While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:

  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.

scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

About

Tutorials for learning scverse

scverse-tutorials.readthedocs.io/en/latest/

Resources

Readme
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Activity

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0 stars

Watchers

0 watching

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0 forks
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
scverse tutorials
Documentation
On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains:
  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core
and ecosystem packages (see docs)
Adding tutorials
If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request
in the next open community meeting and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
  • all featured packages must be scverse core or
approved ecosystem packages. This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
Structure of external tutorials
While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:
  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.
scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
About
Tutorials for learning scverse
scverse-tutorials.readthedocs.io/en/latest/
Resources
Readme
License
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
scverse tutorials
Documentation
On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains:
  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core
and ecosystem packages (see docs)
Adding tutorials
If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request
in the next open community meeting and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
  • all featured packages must be scverse core or
approved ecosystem packages. This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
Structure of external tutorials
While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:
  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.
scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
About
Tutorials for learning scverse
scverse-tutorials.readthedocs.io/en/latest/
Resources
Readme
License
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
scverse tutorials
Documentation
On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains:
  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core
and ecosystem packages (see docs)
Adding tutorials
If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request
in the next open community meeting and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
  • all featured packages must be scverse core or
approved ecosystem packages. This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
Structure of external tutorials
While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:
  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.
scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
About
Tutorials for learning scverse
scverse-tutorials.readthedocs.io/en/latest/
Resources
Readme
License
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
scverse tutorials
Documentation
On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains:
  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core
and ecosystem packages (see docs)
Adding tutorials
If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request
in the next open community meeting and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
  • all featured packages must be scverse core or
approved ecosystem packages. This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
Structure of external tutorials
While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:
  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.
scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
About
Tutorials for learning scverse
scverse-tutorials.readthedocs.io/en/latest/
Resources
Readme
License
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
scverse tutorials
Documentation
On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains:
  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core
and ecosystem packages (see docs)
Adding tutorials
If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request
in the next open community meeting and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
  • all featured packages must be scverse core or
approved ecosystem packages. This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
Structure of external tutorials
While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:
  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.
scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
About
Tutorials for learning scverse
scverse-tutorials.readthedocs.io/en/latest/
Resources
Readme
License
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
scverse tutorials
Documentation
On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains:
  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core
and ecosystem packages (see docs)
Adding tutorials
If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request
in the next open community meeting and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
  • all featured packages must be scverse core or
approved ecosystem packages. This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
Structure of external tutorials
While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:
  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.
scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
About
Tutorials for learning scverse
scverse-tutorials.readthedocs.io/en/latest/
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scverse tutorials
Documentation
On scverse.org/learn, we aim at providing a comprehensive overview of analyses that can be
performed with scverse core and ecosystem packages.
To this end, this repository contains:
  • a registry for tutorials listed on scverse.org/learn (see tutorial-registry)
  • shared tutorials that complement more specific tutorials provided by invidiual core
and ecosystem packages (see docs)
Adding tutorials
If you believe a tutorial should be added to scverse.org/learn, please open an issue. We will discuss the request
in the next open community meeting and potentially suggest
improvements.
To be added to our website, tutorials must fulfill at least the following requirements:
  • all featured packages must be scverse core or
approved ecosystem packages. This does not apply to packages that are not
specific to omics data analysis (e.g. pandas, seaborn).
  • the notebook author agrees to maintain the tutorial in the future and is reachable via zulip.
  • the notebook contains a backlink to scverse.org/learn
  • the notebook is self-contained: All required example data is downloaded as part of the tutorial
You can easily check your changes to tutorials or the registry locally:
hatch run docs:build # for tutorial notebooks
hatch run registry:validate # for the tutorials registry
Structure of external tutorials
While we do not mandate a specific structure for tutorials, a good tutorial typically comprises the following sections:
  1. General header: The tutorial should have a general header that corresponds to the analysis.
  2. Brief introduction: The tutorial should introduce the package, the analysis motivation and potentially biological background.
  3. Requirements to run the notebook: Special computational requirements like memory or GPUs should be specified. Any required input from other notebooks should also be listed here.
  4. Package imports: All required packages should now be imported.
  5. General setup: General settings such as plotting settings or ignored warnings should be set up here.
  6. Data loading: Any required datasets should be loaded here. Ideally with stable links.
  7. Data preprocessing: Any data preprocessing should be done here. Depending on the method this step can be skipped.
  8. Package specific tutorial: The tutorial for the package should contain a healthy mix of text and code to guide the user through the analysis.
  9. Link to other important tutorials/packages/sources of information: Link to any other tutorials that might be of interest or the corresponding https://sc-best-practices.org chapter.
  10. References: Any referenced papers should show up in references section.
  11. Acknowledgements: All contributing authors and experts should be named.
scverse-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
About
Tutorials for learning scverse
scverse-tutorials.readthedocs.io/en/latest/
Resources
Readme
License
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages