Advanced transcriptome analysis and R data visualization hot registration (2022.10)

福利公告：为了响应学员的学习需求,经过易生信培训团队的讨论筹备,Now the schedule《高级转录组分析和R数据可视化》于2022年10月21-23 线上/线下课程 (Class is through tencent meeting broadcast live line class,实时互动,And recorded a video replay,Indefinitely to watch).报名参加线上直播课的老师可在365Days to choose to join a line with the course of class .Looking forward to and you met online.

• 宏基因组线上/线下开课时间：2022/8/19-2022/8/21

• 临床基因组学线上/线下开课时间：2022/8/26-2022/8/28

• 扩增子线上/线下开课时间：2022/10/14-2022/10/16

• 转录组线上/线下开课时间：2022/10/21-2022/10/23

• 报名链接：http://www.ehbio.com/Training/

Transcriptome analysis is one of the most widely used high throughput sequencing analysis technology.Common design is a comparison between different samples,寻找差异基因、Marker gene、Synergy changes in gene、Differences between the new transcription splicing and the,并进行结果可视化、功能注释和网络分析等.

The sequencing analysis of the transcriptome is relatively mature,从RNA提取、构建文库、Computer sequencing results to parse can complete yourself,And in a professional company in.

Overall the transcriptome analysis process is simple,序列比对-This transcription splicing (可选)-表达定量-差异基因-功能富集-定制分析.The entire link fluidity,Can be used as the most begin to contact high-throughput sequencing learning one of the most appropriate technology.

But the key and difficult point is to understand how these processes are,有什么需要注意的,The result how to interpret,Subsequent analysis how to do.Only yourself to use these,Be understanding.And understand a,Other types of analysis to do again,也会轻松很多.

The experimental design is the important reference and at least3个生物学重复,And select the appropriate sequencing flux.ENCODEFor repeat betweenSpearman correlation值大于0.9 (Genetic background of biological repeat the correlation coefficient is greater than0.8).Quantitative evaluation gene expression and transcription atlas similarity only need medium sequencing depth;Research new transcript and alternative splicing requires deeper sequencing;Generally longRNA-seqLibrary sequencing depth meet可用reads在20-30 million (If the testPE150,Conversion into a base for6G-9G).

It is important to note, another sequencing batch effect,Ensure your samples at the same time to deal with、RNA同时提取、At the same time build library and computer sequencing.Although these links is not always controlled by the us,But record the corresponding operation time and batch,The final expression mapping with experimental parameters关联展示 (The use of introduce our热图简化或高颜值免费在线绘图工具升级版来了~~~),To ensure the result was not affected by the presence of trial processing batches.ENCODEPlans to an article in the comparison of the different groups of mice and humans expression spectrum similarity is rather than the organization as a result of the samples according to the species together,It is not in conformity with the previously believed the conservatism of the developmental pathway.Later found to be sequencing batch pounding ghost,Do the batch effect correction after,Express map according to the organization rather than the species together（高通量数据中批次效应的鉴定和处理 - 系列总结和更新）.

Sequencing link usually do not need their operation,Sequencing companies are very mature,但The principle of sequencing需要知道.This will affect the subsequent analysis parameters selection,比如知道What is inserted into the fragment size,What is a chain of specificity sequencing,What will be接头序列,Double side sequencing how to measure, etc.

获得数据后,Data transmission and quality evaluation is involved(Also include how to download data from public database)And file format conversion.FASTQFormat interpretation and evaluationSome mention.The significance of quality evaluation is to build library from the Angle of the sequencing quality evaluation, and sequencing of success,Guide joint and low quality base to remove.This step parameter control strictly or not influence on subsequent than there will be a,At the same time also will be affected by subsequent analysis tool of choice.对Linux系统A certain degree of understanding,Is the basis of the work.

39A transcriptome analysis tools,120Kind of combination evaluation(Transcriptome analysis tool which is strong)Tells the story of how to choose、Evaluation of appropriate alignment tools,Sequence assembly tools,Quantitative tools and variance analysis.Worth before the formal analysis of,仔细阅读.Assessment of other similar articles,There are a few,Can read along with all the,So late in the analysis of the selection and use of the tool only more handy.

Tool to compare articles usually tell what you do,Don't tell you what is the reason for this,And segment from each step and have a lot of small details need to pay attention to,Such as in than link will involve：Different samples of how to choose the suitableGenome and annotation file,What kind of software supportJunction reads的比对,什么样的比对率是合适的,Than how the quality,测序中RNAPresence of degradation or select preferences,How sequencing saturation, etc.

These may not be reflected in the final result,But all is to ensure that the results reliability of the late must do.2002年诺贝尔奖得主Sydney BrennerRemind that had been made to data analysis to doGarbage in, Garbage out.The software is dead,Provides a format correct input,就可以得到输出,But the output correctly or not,Have to rely on people's experience to judge the.

In the back of the differences in gene identification stage,There is also theFPKMValue into an integer and then submitted to theDESeq2做分析的,The software is not an error,但结果不对.Or can run along the tutorialDEseq2分析,But with their own data don't know how to start （DESeq2Differences in genetic analysis and batch effect to remove）.All these problems need to be continuous trial and error in the process of practice、Read more articles and tutorials to correct.

Did a test to see to know how much？

1. 120Points of the transcriptome questions（The first answer）

2. 120Points of the transcriptome questions（The second answer）

3. 120Points of the transcriptome questions（The third part of the answer）

This, of course, is a time-consuming process,那么有没有一个更好的方式呢？

那就是第十七期高级转录组分析和R数据可视化

（Part of the video can be inBFree standing space view：https://www.bilibili.com/video/BV1rD4y1272a）

基于以往16Once the transcriptome training,The transcriptome course content mature,Can in the shortest possible time to learn the most knowledge.

Before the training focus has in the previous process analysis,To do this time adjust,Process analysis to sort out a clear input、输出框架,Packaged process scripts and parameters note,Fast operating from source.Key to adjust to the subsequent analysis of the custom and the drawing,Involved in commonGO分析、Clustering of single-cell transcriptome analysis、Matching samples and time series samplesGSEA富集分析、结合motifPrediction and transcription factorChIPThe regulation of network analysis、Custom graphics、Cytoscape进行富集分析、调控网络、Visual pathway,Target gene screening and visualization, WGCNAWeighted total express network analysis,机器学习,ceRNA网络.

Each section with clear思维导图Convenient understanding input、输出、命令、参数和注意事项.

The follow-up in our training group will also provideLong-term free graphics cooperation service,Share with you the drawing code,一起学习.

第十七期高级转录组分析和R数据可视化在于2022年4月8Online/Offline class at the same time,The system about based on and is not based on the comparison of the transcriptome analysis process,From the original data to the expression of matrix、差异基因、可变剪接、富集分析、Weighted total express network、通路分析、可视化绘图,ceRNA,Machine learning and a series of common operation,Both theory and practice.

（访问链接：www.ehbio.com/Training 抢先报名）

课程大纲

请详细阅读课程简介,如果以下内容您全精通,不必参加此培训.

每节课1小时一个主题,理论结合实战,学懂原理,实战实操,All old driver experience for many years、Process and code selfless share,手把手带您快速入门、节约宝贵的时间,助力科研成果早日产出.

下面是课程安排,本课程一共3天,每天6节课,共18节课,全部课程均理论与实战结合(只要课上讲的都是可以学会并自己实现的分析).如11代表第一天第一节课,26代表第二天第六节课,41For two weeks after the regular online video FAQ and subsequent discussion group of permanent answer.

This course is the first13期,经过12次迭代更新,The whole process more mature,Can in the shortest possible time to learn the most knowledge.3天时间,老司机带您完成自学需要3个月甚至是1年的崎岖之路,Help you really play the transcriptome analysis,并根据自己课题的背景优化分析方案.

编号	内容	简介
01	视频学习Linux基础	Paid to provide learning video
02	视频学习R基础	Paid to provide learning video
03	软件安装	Paid to provide installation video
04	Pay the full price	Provide full video as a preview
11	Summary of the transcriptome	The transcriptome design、应用、批次效应等
12	Introduction of the transcriptome analysis process	基于/Based on the comparison analysis process of the speech
13	SalmonQuantitative real	Based on comparing not directly quantitative gene transcription and the expression of
14	差异基因分析	DESeq2More groups of different genetic analysis、热图、火山图
15	GOEnrichment of analysis, and visualization	泡泡图、热图、网络图、弦图
16	GSEAEnrichment of analysis, and visualization	Grouping and time sequenceGSEA
21	Secondary and tertiary sequence principle is introduced	Build library sequencing process and matters needing attention
22	The original data than back to the genome	STARThe comparison and quantitative
23	基于count的差异基因	Batch effect appraisal and remove
24	LinuxUnder the transcriptome environment configuration	Conda软件安装、配置
25	The genome browser data visualization	IGV呈现reeads比对、峰图、Sashimiplot
26	Transcription the assemblingStringTie	Alternative splicing analysisrMATS
31	Common graphing and interpreting the	Illustrator制作CNS标准图版
32	WGCNAWeighted total gene expression	Network analysis associated with character
33	非编码lncRNA鉴定	ceRNA分析 (miRNA-lncRNA-gene调控)
34	No arguments transcriptome analysis	Trinity组装 eggnog注释
35	Transcription regulation analysis	转录调控网络
36	Marker基因鉴定	PCA,随机森林
41	答疑-线上	答疑、考试内容串讲

教程内容简介如下：

Transcriptome analysis platform building

服务器平台：没有软件的计算机只是一堆废铁,No transcriptome analysis system of server and data analysis didn't have anything to do with you.Want to set up a complete set of the transcriptome analysis process,网上的资源即零散、又稀少.易生信团队将分享多年经验摸索优秀软件和布置技巧,并分享全部源代码,让你在主流Linux服务器系统(Ubuntu 16/18.04,CentOS7等主流发行版)On fast decorate focus group analysis processes rely on dozens of commonly used software、几百个依赖的R和Python包,轻松拥有专业分析平台.

Personal computer platforms：高通量测序所谓的大数据,Are in the process of original data and analysis of large size,Computing resources demand more,But not results file.Usually get samples gene expression transcriptomic analysis table、New transcript and non-coding genes,这些表格是下游分析、高级分析以及个性分析的起点,绝大部分工作在我们的笔记本上是可以搞定的,只是很多人并不知道如何入手.

其实你的个人电脑就是数据表(丰度矩阵)统计分析的利器.易生信团队独创实现了跨平台的分析流程,在大家的WindowsNotebook can easily realize the transcriptome analysis、可视化的绝大多数分析,Courses take you easily on their laptop data statistical analysis and visualization platform,基于目前最主流的Win10进行优化和测试,让笔记本秒变数据分析可视化平台.

Basic knowledge of raw letter

有了生信分析平台,如何灵活运用还是要学点独门绝学的.21世纪最重要的是人才,人才最好掌握三门语言,将让你人生立于不败之地,在任何团队中都是不可或缺的人才.这三门语言就是中文、英文和计算机语言.中文每天都在用在学,英文对于博士也至少接触了10年以上并能应用于阅读和写作文献,而编程语言大家大学阶段都学过Visual Basic、Visual Foxpro、或C语言,但能在工作中应用的绝对凤毛麟角.更何况这些语言在生命科学领域是非常低效的,不提倡学习.

生信中最常用的三类语言是·Shell + R + Python/Perl·,前两门是基础,Biologists need to graspShell和R语言基础知识,保证你完成项目分析.我们在课上将同时讲解Biologists need to graspShell和R语言基础知识,保证你高效、The use of stable transcriptome analysis platform、保证大数据分析和后期可视化至发表阶段所需的技能.In the end, we provide learning video for preparation in advance.

当你利用几个小时,走进大数据分析和可视化的大门后,你将发现一个全新的世界.很多人会感觉相见恨晚,爱上分析,从此走向人生的快车道.即使你对编程不感兴趣,这里面用到的理念也定能让你受益终身,在今后相关分析中事半功倍,比别人更胜一筹.Besides, even nowElementary school students to learnPython了,再不会,孩子都带不好了.

(如果基础薄弱,After the success of the application of payment,可免费Get the basic program,做好准备工作, Let the program to be our good tool rather than a stumbling block to learning new things.)

图表解读和绘制专题

针对很多老师缺少系统的生信背景,看不懂分析文章图表,更对绘制各式图表手足无措的情况,在培训时,我们将结合发表的高水平文章,进一步讲解16种常用分析图的原理和使用范围,让你不仅读懂图,更知道如何应用于自己的研究,并亲自轻松完成绘图.

针对大家使用R语言绘图学习时间成本较高的问题,易生信团队针对常用16种图开发了免费绘图网站,一键出图,更可鼠标点选参数修改图形的个性样式.

Published is an indispensible part of scientific research process,Published results without graphics display again.文章图表排版是否整齐规范、协调一致、重点突出对一篇文章的发表也是有不少贡献的.之前推出的Articles published figure changes and layoutA presentation part graphics editing and typesetting operator,This training will also practice from the original shape、To the details and layout of the entire process and the matters needing attention.

Senior transcriptome analysis

1. WGCNA基因共表达分析,WGCNA基因、Phenotypic correlation analysis

2. Cytoscape绘制ceRNA、转录调控、Protein protein interaction network

3. Cytoscape A total of express network rendering

4. KEGG/ReactomeAccess map figure expression

5. Mining and gene interactions of literature database mining展示

6. GO/GSEA（普通分组、Shape and time sequence number）The custom of analysis

The application of the transcriptome、Design and case sharing

The transcriptome is very regular analysis,Is the basis of introduction to high throughput sequencing analysis.This section covers the entire application of high-throughput sequencing technology,The experimental principle of high-throughput sequencing technologies include测序通量、Sequencing batch、测序原理等.

1. The transcriptome studies technology introduction

2. The transcriptome study experimental design and sequencing principle、注意事项

3. 二代、Three generations of sequencing process and principle of analytical

4. The transcriptome study case analyzing

5. Online resources gene expression database

Transcriptome analysis process of actual combat

1. Transcriptome analysis process assessment

2. Sequencing data quality assessment and cleaning

3. Based on comparing the差异基因分析

4. Based on comparing the difference of gene analysis

5. 转录本组装、Alternative splicing analysis and non codingRNA鉴定

6. 目标基因GSEA/GO富集分析

学习完本课程,你能得到什么？

1. Deep understanding from the basic ideas of biological sequence data and analysis process

2. Senior transcriptome analysis, and visualization of the complete process

3. Applied to the analysis of every field experience、Level of code and published the results of the visual

往期精彩回顾

Students mainly come from universities and colleges in China and the director of the institute、教授、副教授、Research institute and the undergraduate,也有来自茅台、五粮液、安琪酵母、华为等大厂的科研人员,There are even overseas Chinese have traveled long distances from the United States、欧洲、澳州、新西兰、Singapore fly to Beijing to participate in the project learning conference.

主讲教师

陈同,博士,2015毕业于中科院遗传与发育生物学研究所,生物信息专业博士,在Cell Stem Cell (IF=23.2,第一作者兼封面文章),Nucleic Acids Research X 3,Nature communications, Protein& Cell, Stem Cells and Development等高水平杂志以第一作者或主要作者发表文章,Operating one hundred thousand people focus《生信宝典》微信公众号,给你不一样的学习生信体验.

授课模式

线上线下同步开课,Online using tencent live meeting.The whole process will record the screen,Video can be indefinitely to watch,For the follow-up study repeatedly watched.

本课程以讲解流程和实际操作为主,采用独创四段式教学,All packaging good code to share,随处可用：

• 第一阶段 3天集中授课;

• 第二阶段 自行练习2周;

• 第三阶段 在线直播答疑;

• 第四阶段 培训视频继续学习;

• 实现教-练-答-用四个环节的统一协调.

培训时间

每天早9点到晚5点

授课地点

Beijing xicheng district near the drum tower（Gulou subway station around1公里）.

线上线下同步开课,Online using tencent live meeting.The whole process will record the screen,Video can be indefinitely to watch,For the follow-up study repeatedly watched.

课程价格

1. 开课两周前报名 4500 元/人

2. 名额有限,每次课程报名满40人后自动关闭报名通道

3. 提供易汉博基因科技实习机会或工作机会

课程福利

1. Offline seats according to sign up andPayment or advance payment success顺序从前到后龙摆尾式排序 （Online live no row of seats）

2. Give corresponding courses to issue a video lesson (http://bioinfo.ke.qq.com)

3. 多人 (N,10>N>1) 组团报名并同时缴费,每人还可减免N-1百元 (最高500)

4. Training data and script byQQ群文件共享

5. Attached to the recommended language share corresponding admissions information to the circle of friends,截图发到[email protected] 可获得200元生信宝典腾讯课堂课程优惠券（可拆分供多个课程使用）

6. 易生信同时推出多门相关课程,连报优惠——同时选2Course the reduction100;

   Three classes of each reduction200,4Door and above the reduction300.

7. Due to favourable activity is timeliness,All offers will be subject to registration system eventually counted.
   

注意事项 *

1. 需自备笔记本电脑,推荐使用win10系统,4G以上内存(推荐8G).

2. 培训班所有数据,文档为内部资料,仅供参阅,未经允许不得翻印外传登刊

3. 上课期间禁止录音,录像

4. 成功付款的学员,若临时有紧急事情不能到来的,可申请延期,更换后续培训班;

   也可申请退款

5. 若开课2周 (含) 前申请退款可退还85%费用;

   开课3个工作日 (含) 前申请退款退还70%的费用 (若已开发票需承担相应手续费)

6. 不可先延期再退款

更多课程的详细介绍,请扫描下方二维码.

复制以下链接http://www.ehbio.com/Training/ 或 点击阅读原文跳转报名页,成为实验中不可或缺的人,赶快报名吧！