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| <!DOCTYPE html> | ||
| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · ISCHIA.jl</title><meta name="title" content="Home · ISCHIA.jl"/><meta property="og:title" content="Home · ISCHIA.jl"/><meta property="twitter:title" content="Home · ISCHIA.jl"/><meta name="description" content="Documentation for ISCHIA.jl."/><meta property="og:description" content="Documentation for ISCHIA.jl."/><meta property="twitter:description" content="Documentation for ISCHIA.jl."/><meta property="og:url" content="https://aadimator.github.io/ISCHIA.jl/"/><meta property="twitter:url" content="https://aadimator.github.io/ISCHIA.jl/"/><link rel="canonical" href="https://aadimator.github.io/ISCHIA.jl/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>ISCHIA.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></li><li><a class="tocitem" href="man/basics/">Basic Usage</a></li><li><a class="tocitem" href="man/seurat_conversion/">Convert Seurat Objects</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="library/types/">Types</a></li><li><a class="tocitem" href="library/functions/">Functions</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/aadimator/ISCHIA.jl/blob/main/docs/src/index.md#" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="ISCHIA"><a class="docs-heading-anchor" href="#ISCHIA">ISCHIA</a><a id="ISCHIA-1"></a><a class="docs-heading-anchor-permalink" href="#ISCHIA" title="Permalink"></a></h1><p>This package is a reimplementation of the ISCHIA LR interaction algorithm in Julia. The original implementation is in R and can be found <a href="https://github.com/ati-lz/ISCHIA">here</a>. The algorithm is described in the paper <a href="https://www.embopress.org/doi/full/10.1038/s44320-023-00006-5">Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)</a>. </p><p>In the original implementation, the LR interaction part of the algorithm is very slow and can take days to run on large datasets. This package aims to speed up the LR interaction part of the algorithm by using Julia's speed and parallelism. For comparison, the original implementation took almost 3 hours to run on their toy/smaller dataset, while the same dataset took around 6 seconds to run on this package.</p><p>Once the LR interactions are calculated, the rest of the plotting and analysis can be done in R using the original package.</p><ul><li><a href="man/basics/#First-Steps-with-ISCHIA.jl">First Steps with ISCHIA.jl</a></li><li class="no-marker"><ul><li><a href="man/basics/#Setting-up-the-Environment">Setting up the Environment</a></li><li><a href="man/basics/#Load-the-Libraries">Load the Libraries</a></li><li><a href="man/basics/#Load-the-Data">Load the Data</a></li><li><a href="man/basics/#Filter-LR-Network">Filter LR Network</a></li><li><a href="man/basics/#Calculate-LR-Enrchiment">Calculate LR Enrchiment</a></li><li><a href="man/basics/#Display-Calculated-LR-Encrichment-Scores">Display Calculated LR Encrichment Scores</a></li><li><a href="man/basics/#Find-Differentially-Occurring-LR-pairs">Find Differentially Occurring LR pairs</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/basics/">Basic Usage »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.6.0 on <span class="colophon-date" title="Friday 30 August 2024 15:06">Friday 30 August 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> | ||
| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · ISCHIA.jl</title><meta name="title" content="Home · ISCHIA.jl"/><meta property="og:title" content="Home · ISCHIA.jl"/><meta property="twitter:title" content="Home · ISCHIA.jl"/><meta name="description" content="Documentation for ISCHIA.jl."/><meta property="og:description" content="Documentation for ISCHIA.jl."/><meta property="twitter:description" content="Documentation for ISCHIA.jl."/><meta property="og:url" content="https://aadimator.github.io/ISCHIA.jl/"/><meta property="twitter:url" content="https://aadimator.github.io/ISCHIA.jl/"/><link rel="canonical" href="https://aadimator.github.io/ISCHIA.jl/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>ISCHIA.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></li><li><a class="tocitem" href="man/basics/">Basic Usage</a></li><li><a class="tocitem" href="man/seurat_conversion/">Convert Seurat Objects</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="library/types/">Types</a></li><li><a class="tocitem" href="library/functions/">Functions</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/aadimator/ISCHIA.jl/blob/main/docs/src/index.md#" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="ISCHIA"><a class="docs-heading-anchor" href="#ISCHIA">ISCHIA</a><a id="ISCHIA-1"></a><a class="docs-heading-anchor-permalink" href="#ISCHIA" title="Permalink"></a></h1><p>This package is a reimplementation of the ISCHIA LR interaction algorithm in Julia. The original implementation is in R and can be found <a href="https://github.com/ati-lz/ISCHIA">here</a>. The algorithm is described in the paper <a href="https://www.embopress.org/doi/full/10.1038/s44320-023-00006-5">Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)</a>. </p><p>In the original implementation, the LR interaction part of the algorithm is very slow and can take days to run on large datasets. This package aims to speed up the LR interaction part of the algorithm by using Julia's speed and parallelism. For comparison, the original implementation took almost 3 hours to run on their toy/smaller dataset, while the same dataset took around 6 seconds to run on this package.</p><p>Once the LR interactions are calculated, the rest of the plotting and analysis can be done in R using the original package.</p><ul><li><a href="man/basics/#First-Steps-with-ISCHIA.jl">First Steps with ISCHIA.jl</a></li><li class="no-marker"><ul><li><a href="man/basics/#Setting-up-the-Environment">Setting up the Environment</a></li><li><a href="man/basics/#Load-the-Libraries">Load the Libraries</a></li><li><a href="man/basics/#Load-the-Data">Load the Data</a></li><li><a href="man/basics/#Filter-LR-Network">Filter LR Network</a></li><li><a href="man/basics/#Calculate-LR-Enrchiment">Calculate LR Enrchiment</a></li><li><a href="man/basics/#Display-Calculated-LR-Encrichment-Scores">Display Calculated LR Encrichment Scores</a></li><li><a href="man/basics/#Find-Differentially-Occurring-LR-pairs">Find Differentially Occurring LR pairs</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/basics/">Basic Usage »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Tuesday 26 November 2024 16:58">Tuesday 26 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
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