相信TCGA和ICGC对搞癌症多组学研究的朋友们来说，应该是不陌生了：

• The Cancer Genome Atlas (TCGA)
• International Cancer Genome Consortium (ICGC)

海量的数据对绝大部分研究者来说只能是望洋兴叹，所以英国癌症中心一直在为推广NGS技术产生的各种各样的数据分析而努力，近3年的生信暑期学习班含金量颇高。而且在朋友圈看到好几个人分享这个生信暑期学习班，有必要我在生信技能树也专门分享一下。

我简单看了看目录，推荐指数4颗星，这个英国癌症中心的生信暑期学习班这3年的内容，都快赶上我在生信技能树录制的免费学习视频了。他们做的很不容易了，这是我第一次夸奖他们，希望我把握好了分寸。不过也可以理解，毕竟英国癌症中心是一个机构嘛，那么多牛人。

你可以对比一下英国癌症中心的生信暑期学习班跟我们生信技能树的全栈生信工程师教学视频

我觉得差距不大了，而且 他们还在努力，希望大家有机会可以参加2020的英国癌症中心的生信暑期学习班。

• 全国巡讲全球听（买一得五） ，你的生物信息学入门课
• 生信技能树的2019年终总结 ，你的生物信息学成长宝藏
• 2020学习主旋律，B站74小时免费教学视频为你领路

2017学习班主题是癌症基因组变异

CRUK Bioinformatics Summer School 2017，时间是 24th - 28th July 2017，课程链接是：

• https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/

Day One 09:30 - 17:00

• 09:30 - 10:00 Course Introduction
• 10:00 - 11:30 R crash course
• 11:30 - 12:30 Overview of Cancer Genomics
• 12:30 - 13:30 LUNCH (provided)
• 13:30 - 14:30 Understanding raw sequencing reads
• 14:30 - 15:00 Understanding aligned reads
• 15:00 - 16:00 Introduction to IGV
• 16:00 - 17:00 Dealing with sequencing data in R

Day Two 09:30 - 17:00

• 09:30 - 10:30 Calling Germline SNVs lecture
• 10:30 - 12:30 Calling Germline SNVs
  • Calling Germline SNVs
  • Working with VCF Files
  • Solutions to vcf exercises
• 12:30 - 13:30 LUNCH (provided)
• 13:30 - 17:00 Copy-number analysis
  • Copy Number Analysis Lecture
  • Copy Number Analysis Practical
• 18:00 - .. Punting trip (weather permitting)

Day Three 09:30 - 17:00

• 09:30 - 10:15 Somatic SNV calling (lecture)
• 10:15 - 10:45 Somatic SNV calling (practical)
• 11:00 - 11:40 SNV Filtering (lecture)
• 11:40 - 12:30 Assessment and visualiation of SNVs (practical)
  • Notes/solution for SNV assessment practical
• 12:30 - 13:30 LUNCH (provided)
• 13:30 - 14:00 Summary of practical and discussion
• 14:00 - 14:30 Annotating and prioritsing SNVs (lecture)
• 14:30 - 16:30 Annotating and prioritsing SNVs (practical)
• 16:30 - 17:00 Somatic indels (lecture)

Day Four 09:30 - 17:00

• 09:30 - 11:30 Structural Variants
• 11:30 - 12:30 Introduction to data portals
• 12:30 - 13:30 LUNCH (provided)
• 13:30 - 14:00 Mutational signatures lecture
• 14:00 - 16:00 Mutational signatures and cohort analyses (TCGA) practical
• 16:00 - 17:00 Running an entire somatic calling pipeline with “docker”

Day Five (1/2 day) 09:30 - 12:30

• Useful Resources
• 09:30 - 12:30 Open-ended;
  • Review results of a somatic-calling pipeline
  • Get advice on analysing your own data
  • Installing software on your own laptop
  • Completing exercises from previous days
  • Any other outstanding questions you might have
• 12:30 - 13:30 LUNCH (provided)

2018年主题是表观调控

CRUK Bioinformatics Summer School 2018: Functional Genomics 时间是：23rd - 27th July 2018: Craik-Marshall Room, Downing Site, University of Cambridge，链接是：

• https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2018/

Day 1 (July 23rd)

• 09:30 Course Introduction
• 09:30 - 10:30; Introduction to Functional Genomics
• 10:30 - 12:30;Introduction (Recap) of R and Bioconductor
• 12:30 - 13:30; LUNCH
• 13:30 - 14:30 Principles of Experimental Design
• 14:30 - 17:00;
• Data processing for Next Generation Sequencing
  • Lecture 1: Introduction to next generation sequencing (2.30- 2.45pm)
  • Lecture 2: Brief introduction to file formats (2.45- 3.00pm)
  • Lecture 3: Quality control and artefact removal (3.00- 3.45pm)
  • Practical 1: learn to use FastQC and Cutadapt (20 min) on a sample dataset
  • Lecture 4: Short read alignment and Quality Control (3.45-5.00pm)
  • Practical 2: Alignment of a ChIP-seq dataset to a reference genome using BWA OR Bowtie2 and a RNA-seq dataset to STAR (45 min)

Day 2 (July 24th)

Please note we use several Rstudio Notebook html files as material for the RNAseq course. To obtain the source code (.Rmd file) you can simply click on the code button in the top right-hand corner).

• 09:00 - 09:30;
  • Introduction to RNA-seq
• 09:30 - 11:00;
  • Counting
  • Importing and QC of RNA-seq data
• 11:00 - 12:30 Linear models & differential expression
  • Slides
  • Linear models html nb
• 12:30 - 13:30; LUNCH
• 13:30 - 15:00; Linear models & differential expression
• 15:00 - 17:00
  • Differential expression analysis with DESeq2

Day 3 (July 25th)

• 09:30 - 11:00; Annotation and Visualisation of Differential Expression
• 11:00 - 12:30; Gene set analysis and Gene Ontology testing
• 12:30 - 13:30; LUNCH
• 13:30 - 16:30; Single Cell RNASeq ‘taster’
  • Introduction to single-cell sequencing
  • QC and normalization Practical.
  • Single cell population identification Practical (Rmd file)
  • Single cell population identification Practical (html file)

NB We do not have sufficient time to teach this entire course in half a day. However, some concepts are covered in the Bulk RNASeq course and we provide the link to the full materials. Please note, that on occasions where all of the material was used, it resulted in a five-day course(!). We will teach topics that should be of interest even to those not interested in single-cell work.

SOCIAL: Punting trip - leave from Mill Lane punting site at 18:00 (~10 min walk from Craik-Marshall) Google Map. Scudamore’s Web-site & Mill lane map.

Day 4 (July 26th)

• ChIP-seq data analysis
  • Lecture 5: Introduction to ChIP-seq (9.30-10.00pm)
  • Lecture 6: Peak Calling (10.00-11.00pm)
  • Practical 3: Peak calling using MACS2 (30 min)
  • Lecture 7: Differential binding analysis (11.00-12.30pm)
  • Practical 4: THOR (and Diffbind) (20 min)
  • Lecture 8: Quality control methods for ChIP-seq (1 hr)
  • Practical 5: ChIPQC package (30 min)
  • Practical 6: Integrative Genome Viewer (30 min) LUNCH (12.30-1.30pm)
  • Lecture 9: Downstream analysis of ChIP-seq (1.30-3.15pm)
  • Practical 7: Downstream analysis of ChIP-seq (30 min)
  • Practical 8: Identifying direct targets of transcription factors with Rcade (30 min)
  • Lecture 10:: Useful software utilities for the analysis of genomic data (4.30-5.00pm)

SOCIAL: Summer School evening meal & Reception at the nearby Downing College at 18:00 to 22:30.. If you do not wish to attend this meal (free to attendees) then please let us know ASAP. Smart casual dress. http://www.dow.cam.ac.uk Downing College, Regent Street, Cambridge, CB2 1DQ (Site map in link below)
Drinks Reception 18:00- 19:45 West Lodge
Dinner 19:45 -22:30 Grace Howard Room

Day 5 (July 27th)

• 09:30 - 12:30; A room in C-M building will be available for storing your baggage (There will be signage)
• ATAC-seq and Epigenomics
  • Practical 9: Useful software utilities for the analysis of genomic data (9.30-10.30am)
  • Lecture 11 ATAC-seq data analysis (10.30-11.30am)
  • Practical 10: ATAC-seq analysis (30 min)
  • Lecture 12 Introduction to Epigenomics and Chromatin Interactions (11.30-12.30)
• 12:30 - 13:30; LUNCH

2019年主题与2018年一样

CRUK Bioinformatics Summer School 2019: Functional Genomics时间是：15th - 19th July 2019: Craik-Marshall Room, Downing Site, University of Cambridge，链接是

• https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2019/

Day 1 (July 15th)

Breakfast at Downing College is at 8.45-9.15am.

C-M Training room.

• 09:30 Course Introduction
• 09:30 - 10:30; Introduction to Functional Genomics
• 10:30 - 12:30; Introduction to Bioconductor.
• 12:30 - 13:30; LUNCH
• 13:30 - 14:30 Principles of Experimental Design
• 14:30 - 17:00;
• Data processing for Next Generation Sequencing
  • Lecture 1: Introduction to next generation sequencing (2.30- 2.45pm)
  • Lecture 2: Brief introduction to file formats (2.45- 3.00pm)
  • Lecture 3: Quality control and artefact removal (3.00- 3.45pm)
  • Practical 1: learn to use FastQC and Cutadapt (20 min) on a sample dataset
  • Lecture 4: Short read alignment and Quality Control (3.45-5.00pm)
  • Practical 2: Alignment of a ChIP-seq dataset to a reference genome using BWA OR Bowtie2 and a RNA-seq dataset to STAR (45 min)

Day 2 (July 16th)

• 09:30 - 10:00;
  • Introduction to RNA-seq
• 10:00 - 11:30;
  • Counting
  • Importing and QC of RNA-seq data
  • Challenge Solutions
  • Supplementary Material: Obtaining raw reads from SRA
• 11:30 - 12:30 Linear models & differential expression
  • Slides
  • Annotated Slides
  • Linear models html nb
• 12:30 - 13:30; LUNCH
• 13.30 - 15:00; Linear models & differential expression (cont)
• 15:00 - 17:30
  • Differential expression analysis with DESeq2
  • Challenge Solutions

Day 3 (July 17th)

• 09:30 - 11:00;

• Annotation and Visualisation of Differential Expression

  • Challenge Solutions
  • Supplementary Material: Further visualistations

• 11:00 - 12:30;

• Gene set analysis and Gene Ontology testing

  • Challenge Solutions

• 12:30 - 13:30; LUNCH

• 13:30 -14:00; Prognostic Gene Signatures (RS)

• Slides

• 14:00 – 14:30; Survival Analysis (DL)
  + Slides
  + Annotated Slides
  + R Markdown doc.

• 14:30 – 15:00; Practical: Deriving a Predictive Gene Signature from DEGs

• R Markdown doc.

• 15:00 – 15:30; Issues with prognostic gene signatures (RS)

• Slides

• 15:30 – 16:00;

Practical: Checking gene signatures with SigCheck

• Practical

SOCIAL: Summer School evening meal & Reception at the nearby Downing College at 18:30 to 22:30.. If you do not wish to attend this meal (free to attendees) then please let us know ASAP. Smart casual dress. http://www.dow.cam.ac.uk Downing College, Regent Street, Cambridge, CB2 1DQ (Site map in link below). The college should put up signage to help you find the venue.
The reception is at 6.30pm and dinner at 7.30pm Plus a post-Dinner talk: “Perspectives in AI for Cancer Bioinformatics by Rory Stark”.
Drinks Reception 18:30- 19:30 Grace Howard Room, Dinner 19:30 -22:30 Grace Howard Room

Day 4 (July 18th)

• ChIP-seq data analysis

• Lecture 1a: Introduction to ChIP-seq (9.30-9.45am)

  • Lecture 1b: Introduction to Peak Calling (9.45-10.30am)
  • Practical 1: Peak calling with MACS2 (10.30-11.00am)
  • Lecture 2: Differential binding analysis (11.00-11.30am)
  • Practical 2: THOR (and Diffbind) (11.30-12.00pm)
  • Lecture 3: Quality control methods for ChIP-seq (12.00-12.30pm)

LUNCH (12.30-1.30pm)

• Practical 3: Integrative Genome Viewer (1.30-2.00 min)
  • Lecture 4: Downstream analysis of ChIP-seq (2.00-2.30pm)
  • Practical 4: Downstream analysis of ChIP-seq (2.30-3.15pm)
  • Lecture 5: Introduction to (epi)Genomic data integration(3.15-3.45pm)
  • Practical 5: Data Integration for Genomics (TF direct targets & chromatin modifications) (3.45-5.00 min)

Day 5 (July 19th)

• 09:30 - 12:30; **A room in C-M building will be available for storing your baggage (There will be signage)
• Chromatin Accessibility
  • Lecture 1 Chromatin accessibility and nucleosome occupancy with ATAC-seq (9.30-10.00am)
  • Practical 1: ATAC-seq analysis (10.00-11.00am)
  • Lecture 2: Useful software utilities for the analysis of genomic data (11.00-11.30am)
  • Practical 2: Useful software utilities for the analysis of genomic data (11.30-12.30pm)
• 12:30 - 13:30; LUNCH
• Some of you may now be going to the CRUK Cambridge Centre Graduate Symposium Hope you enjoy it!

文末友情宣传

强烈建议你推荐给身边的博士后以及年轻生物学PI，多一点数据认知，让他们的科研上一个台阶：

• 全国巡讲全球听（买一得五），第二期 ，你的生物信息学入门课
• 生信技能树的2019年终总结 ，你的生物信息学成长宝藏
• 2020学习主旋律，B站74小时免费教学视频为你领路