癌症组学meta分析器具汇总（没代码）
前言：应师姐们的邀请，把大四时做Meta-Analysis的<span style="color: black;">有些</span><span style="color: black;">工具</span>汇总到<span style="color: black;">这儿</span>(<span style="color: black;">亦</span>有<span style="color: black;">有些</span>新的)。其实做分析的<span style="color: black;">工具</span><span style="color: black;">非常多</span>，分析流程大同小异，最<span style="color: black;">要紧</span>的是要明白分析流程的原理和各个参数的<span style="color: black;">道理</span>。<h2 style="color: black; text-align: left; margin-bottom: 10px;">做预后分析的几个<span style="color: black;">网</span></h2>oncoLnc: <a style="color: black;"><span style="color: black;">http://www.</span><span style="color: black;">oncolnc.org/</span></a>Tips：这个是<span style="color: black;">按照</span>某个gene高表达和低表达进行分组，做的预后分析，数据<span style="color: black;">源自</span>于TCGA。<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">Step1:输入感兴趣的gene，submit。</p><div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic4.zhimg.com/80/v2-03d09ce48761adc355103eac6d3675ef_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">Step2：<span style="color: black;">选取</span>癌症，点击Yes Please!(<span style="color: black;">这儿</span><span style="color: black;">必须</span>对癌症的各个缩写熟悉一下啦)</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic2.zhimg.com/80/v2-5d84cdfe2ab5fb593a75a62b8e5b2aed_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">Step3：<span style="color: black;">选取</span>高低表达的分界线（预后分析的<span style="color: black;">重要</span>参数）</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">可选填50/50，即中位数划分。<span style="color: black;">亦</span>有其他划分<span style="color: black;">办法</span>（如均值mean，<span style="color: black;">或</span>上30%，下30%等等），submit后等结果吧。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic3.zhimg.com/80/v2-35c9a423d2e2e54691dbcac30d7455fe_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">Step4:<span style="color: black;">便是</span>出图啦</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic1.zhimg.com/80/v2-73f91b443330a670fcd8b061702bb3d8_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">2. Progene：<a style="color: black;"><span style="color: black;">http://</span><span style="color: black;">genomics.jefferson.edu/</span><span style="color: black;">proggene/</span></a>
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<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">Progene<span style="color: black;">包括</span>了TCGA和GEO的数据。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic2.zhimg.com/80/v2-ab98ef27259192e7542241951f2052a1_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">这个<span style="color: black;">网</span>就<span style="color: black;">必须</span>一步填好所有的Input和参数了。</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">最上面的三个框框，有三种输入格式，可<span style="color: black;">按照</span>自己的<span style="color: black;">状况</span><span style="color: black;">选取</span>。查看单个基因的选<span style="color: black;">第1</span>个输入。</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">第二个框框，<span style="color: black;">选取</span>癌症类型。</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">第三个框框，做预后就<span style="color: black;">不消</span>改。</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">第四个框框，看见那个MEDIAN了吗？<span style="color: black;">便是</span>高低表达的分界线，默认是MEDIAN(中位数)。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic4.zhimg.com/80/v2-76aadad72a3d4f0d1eee1aca296388db_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">点一下，看到有四个选项哦，自己去看各个参数的含义吧，用MEDIAN比较多。</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">我用TP53和BREAST举个例子吧。</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">我在<span style="color: black;">第1</span>个框框输入TP53后，其他不动（默认BREAST和MEDIAN），点击NEXT。就跳出来下面这个界面。<span style="color: black;">这儿</span><span style="color: black;">必须</span>选数据集（<span style="color: black;">通常</span>选all），<span style="color: black;">仅有</span>被选中的，才会画图哦。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic1.zhimg.com/80/v2-237e1257358b6d2faeba61817ae37b40_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">点击SELECT/DESELECT ALL，看到YES前面的小框框打勾后，就<span style="color: black;">能够</span>点击CREATE PLOTS了。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic1.zhimg.com/80/v2-ef328db959580bcafbe1f3e804e79a44_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">最后结果：<span style="color: black;">这儿</span>只展示了<span style="color: black;">第1</span>个结果。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic1.zhimg.com/80/v2-b3a25f97c0a8b7c82a5e1db1940debd4_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<h2 style="color: black; text-align: left; margin-bottom: 10px;"><span style="color: black;">能够</span>做表达分析+预后分析的<span style="color: black;">网</span></h2>GEPIA2:<a style="color: black;"><span style="color: black;">http://</span><span style="color: black;">gepia2.cancer-pku.cn/#</span><span style="color: black;">index</span></a>看到<a style="color: black;"><span style="color: black;">http://</span><span style="color: black;">pku.cn</span></a>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">结尾，就<span style="color: black;">晓得</span>这个是北大<span style="color: black;">研发</span>的<span style="color: black;">工具</span>，<span style="color: black;">不仅</span><span style="color: black;">能够</span>做表达分析，<span style="color: black;">亦</span><span style="color: black;">能够</span>做预后分析（请自己去摸索流程，和前面几个<span style="color: black;">网</span>的流程是<span style="color: black;">同样</span>的，现在有<span style="color: black;">非常多</span>一体化流程的分析<span style="color: black;">网</span>，<span style="color: black;">然则</span>分析的思路都是差不多的，这点自学能力要有，<span style="color: black;">况且</span><span style="color: black;">网</span><span style="color: black;">通常</span>很友好的，不行还有百度不是么）。</p>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">分析流程总共有四个，Single Gene Analysis, Cancer Type Analysis, Custom Data Analysis以及Multiple Gene Analysis。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic2.zhimg.com/80/v2-715d02341b78e25ba60d741ffe6f2275_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">依旧是TP53举例子，做个Single Gene Analysis, 点击 GoPIA! 后，就能看到许多<span style="color: black;">美丽</span>的图了,<span style="color: black;">能够</span>看到TP53在<span style="color: black;">各样</span>癌症里的表达<span style="color: black;">状况</span>，有Dotplot和Barplot(仅展示了Barplot)，还有其他<span style="color: black;">有些</span>信息。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic1.zhimg.com/80/v2-70b7d15632d6cf0632460499831d3878_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">2. chrislifescience: <a style="color: black;"><span style="color: black;">htt</span></a>p://www.<span style="color: black;">chrislifescience.club:3838</span><span style="color: black;">/R/AnnoE2/</span>一个<span style="color: black;">先辈</span><span style="color: black;">研发</span>的<span style="color: black;">网</span>，还有公众号教程（公众号：Chris生命科学小站，原文链接：<a style="color: black;"><span style="color: black;">https://</span><span style="color: black;">mp.weixin.qq.com/s/TeND</span><span style="color: black;">fTPHptnyU4Gah-ASLQ</span></a>），就不搬运了。</p>
<div style="color: black; text-align: left; margin-bottom: 10px;"><img src="https://pic3.zhimg.com/80/v2-28010c21fd1d6f7b5e5d714a0bc35caa_720w.webp" style="width: 50%; margin-bottom: 20px;"></div>
<p style="font-size: 16px; color: black; line-height: 40px; text-align: left; margin-bottom: 15px;">尾声：至于我是怎么做的，当然是R/Bioconductor啦，<span style="color: black;">由于</span>出图风格一致（ggplot2）。后续再整理R代码版本的吧（先挖一个坑，不<span style="color: black;">晓得</span>什么时候填）。</p>
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