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<section id="welcome-to-celloracle-s-documentation">
<h1>Welcome to CellOracle’s documentation!<a class="headerlink" href="#welcome-to-celloracle-s-documentation" title="Permalink to this headline">¶</a></h1>
<p><a class="reference external" href="https://github.com/morris-lab/CellOracle/actions/workflows/build_check.yml"><img alt="GitHub Workflow Status" src="https://img.shields.io/github/actions/workflow/status/morris-lab/CellOracle/build_check.yml?branch=master" /></a> <a class="reference external" href="https://pypi.org/project/celloracle/"><img alt="PyPI" src="https://img.shields.io/pypi/v/celloracle?color=blue" /></a> <a class="reference external" href="https://pypi.org/project/celloracle/"><img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/celloracle" /></a> <a class="reference external" href="https://pypi.org/project/celloracle/"><img alt="PyPI - Wheel" src="https://img.shields.io/pypi/wheel/celloracle" /></a>
<a class="reference external" href="https://pepy.tech/project/celloracle"><img alt="Downloads" src="https://static.pepy.tech/personalized-badge/celloracle?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads" /></a> <a class="reference external" href="https://hub.docker.com/r/kenjikamimoto126/celloracle_ubuntu"><img alt="Docker Pulls" src="https://img.shields.io/docker/pulls/kenjikamimoto126/celloracle_ubuntu?color=orange" /></a></p>
<p>CellOracle is a python library for the in silico gene perturbation analysis using single-cell omics data and gene regulatory network models.</p>
<p>Source code is available at <a class="reference external" href="https://github.com/morris-lab/CellOracle">CellOracle GitHub repository</a> and <a class="reference external" href="https://pypi.org/project/celloracle/">PyPI</a>.</p>
<p>For more information, please read our paper: <a class="reference external" href="https://www.nature.com/articles/s41586-022-05688-9">Dissecting cell identity via network inference and in silico gene perturbation</a></p>
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let valMin = 0.0;
let valMax = 0.025;
let xmin = -12000;
let xmax = 12000;
let ymin = -12000;
let ymax = 12000;
let cmap_array = ["#000000","#020000","#040000","#060000","#080000","#0a0000","#0c0000","#0e0000","#100000","#120000","#140000","#160000","#180000","#1a0000","#1c0000","#1e0000","#200000","#220000","#240000","#260000","#280000","#2a0000","#2c0000","#2e0000","#300000","#320000","#340000","#360000","#380000","#3a0000","#3c0000","#3e0000","#400000","#420000","#440000","#460000","#480000","#4a0000","#4c0000","#4e0000","#500000","#520000","#540000","#560000","#580000","#5a0000","#5c0000","#5e0000","#600000","#620000","#640000","#660000","#680000","#6a0000","#6c0000","#6e0000","#700000","#720000","#740000","#760000","#780000","#7a0000","#7c0000","#7e0000","#800000","#820200","#840400","#860700","#880800","#8a0a00","#8c0d00","#8e0f00","#901000","#921200","#941400","#961700","#981800","#9a1a00","#9c1d00","#9e1f00","#a02000","#a22200","#a42400","#a62700","#a82800","#aa2a00","#ac2d00","#ae2f00","#b03000","#b23200","#b43400","#b63700","#b83800","#ba3a00","#bc3d00","#be3f00","#c04000","#c24200","#c44400","#c64600","#c84800","#ca4a00","#cc4d00","#ce4e00","#d05000","#d25200","#d45400","#d65600","#d85800","#da5a00","#dc5d00","#de5e00","#e06000","#e26200","#e46400","#e66600","#e86800","#ea6a00","#ec6d00","#ee6e00","#f07000","#f27200","#f47400","#f67600","#f87800","#fa7a00","#fc7d00","#fe7e00","#ff8001","#ff8203","#ff8405","#ff8607","#ff8809","#ff8b0b","#ff8c0d","#ff8e0f","#ff9011","#ff9213","#ff9415","#ff9617","#ff9919","#ff9b1b","#ff9c1d","#ff9e1f","#ffa021","#ffa223","#ffa425","#ffa627","#ffa829","#ffab2b","#ffac2d","#ffae2f","#ffb031","#ffb233","#ffb435","#ffb637","#ffb939","#ffbb3b","#ffbc3d","#ffbe3f","#ffc041","#ffc243","#ffc445","#ffc647","#ffc849","#ffcb4b","#ffcc4d","#ffce4f","#ffd051","#ffd253","#ffd455","#ffd657","#ffd959","#ffdb5b","#ffdc5d","#ffde5f","#ffe061","#ffe263","#ffe465","#ffe667","#ffe869","#ffeb6b","#ffec6d","#ffee6f","#fff071","#fff273","#fff475","#fff677","#fff979","#fffb7b","#fffc7d","#fffe7f","#ffff81","#ffff83","#ffff85","#ffff87","#ffff89","#ffff8b","#ffff8d","#ffff8f","#ffff91","#ffff93","#ffff95","#ffff97","#ffff99","#ffff9b","#ffff9d","#ffff9f","#ffffa1","#ffffa3","#ffffa5","#ffffa7","#ffffa9","#ffffab","#ffffad","#ffffaf","#ffffb1","#ffffb3","#ffffb5","#ffffb7","#ffffb9","#ffffbb","#ffffbd","#ffffbf","#ffffc1","#ffffc3","#ffffc5","#ffffc7","#ffffc9","#ffffcb","#ffffcd","#ffffcf","#ffffd1","#ffffd3","#ffffd5","#ffffd7","#ffffd9","#ffffdb","#ffffdd","#ffffdf","#ffffe1","#ffffe3","#ffffe5","#ffffe7","#ffffe9","#ffffeb","#ffffed","#ffffef","#fffff1","#fffff3","#fffff5","#fffff7","#fffff9","#fffffb","#fffffd","#ffffff"];
var render_static_vector = true;
let backgroundColor = 'black';
let axisColor = '#fff';
let showSplitLine = false;
let particleDensity = '64';
let supersampling = '4';
let particleSize = '3';
let particleSpeed = '1';
let opacity = '1';
if (render_static_vector) {
function static_vector_rendering_function(params, api) {
let x = api.value(0),
y = api.value(1),
dx = api.value(2),
dy = api.value(3);
let start = api.coord([x - dx / 2, y - dy / 2]);
let end = api.coord([x + dx / 2, y + dy / 2]);
return {
type: "line",
shape: {
x1: start[0],
y1: start[1],
x2: end[0],
y2: end[1]
},
style: {
lineWidth: 2,
stroke: "#fff",
opacity: 0.2
}
};
}
} else {
let static_vector_rendering_function = null;
}
my_chart_options = {
backgroundColor: backgroundColor,
visualMap: {
show: false,
min: valMin,
max: valMax,
dimension: 4,
inRange: {
color: cmap_array
}
},
xAxis: {
type: 'value',
min: xmin, max: xmax,
axisLine: {
lineStyle: {color: axisColor},
onZero: false,
},
splitLine: {
show: showSplitLine,
lineStyle: {
color: "rgba(255,255,255,0.2)"
}
}
},
yAxis: {
type: "value",
min: ymin, max: ymax,
axisLine: {
lineStyle: {color: axisColor},
onZero: false,
},
splitLine: {
show: showSplitLine,
lineStyle: {
color: "rgba(255,255,255,0.2)"
}
}
},
series: [
{
type: "flowGL",
data: data_array,
supersampling: supersampling,// This parameter affects image resolution,
particleDensity: particleDensity,
particleSize: particleSize,
particleSpeed: particleSpeed,
itemStyle: {
opacity: opacity
}
},
{
type: "custom",
data: data_array,
encode: {
x: 0,
y: 0
},
renderItem: static_vector_rendering_function
}
]
}
})();
var dom = document.getElementById("container");
var myChart = echarts.init(dom, "dark", {
renderer: "canvas",
useDirtyRect: false
});
//console.log(valMin);
myChart.setOption(my_chart_options);
window.addEventListener("resize", myChart.resize);
</script>
</body>
</html>
</section>
<section id="news">
<h1>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h1>
<p>Please look at <a class="reference external" href="https://morris-lab.github.io/CellOracle.documentation/changelog/index.html">Changelog page</a> for all updates history of CellOracle package.</p>
<ul class="simple">
<li><p>03/31/2024: We released celloracle version 0.18.0. Refactoring was done in the motif analysis to improve the stability of the function. Docker image was updated to the latest version of celloracle. From this version, we use python 3.10 in the docker image.</p></li>
<li><p>03/19/2024: We released celloracle version 0.17.1. This update includes a bug fix, refactoring, and new test functions. Now we support Python 3.10.</p></li>
<li><p>02/01/2024: We released celloracle version 0.16.0. Fixed a bug in the Systematic Simulation function to comply with the latest update of pandas.</p></li>
<li><p>07/25/2023: We released celloracle version 0.15.0. This update includes refactoring in the Markov simulation function.</p></li>
<li><p>02/08/2023: CellOracle paper has been published in <a class="reference external" href="https://www.nature.com/articles/s41586-022-05688-9">Nature article</a> ! It is also highlighted in <a class="reference external" href="https://www.nature.com/articles/d41586-023-00251-6">News and Views</a> . Thank you very much to all contributors and users for your help!!!</p></li>
<li><p>02/02/2023: We released celloracle version 0.10.15. We fixed a bug in Motif data loading function.</p></li>
</ul>
</section>
<section id="contents">
<h1>Contents<a class="headerlink" href="#contents" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
<ul>
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