July 22nd - 28th 2020

For Course materials and detailed timetable visit here

Note: You are expected to be familiar with Rstudio, RMarkdown documents and Bioconductor. If you are not then you are advised to work through the material (below) before attending Summer School

• Introduction to Bioconductor.
• Bioconductor answers.
  • source
  • Source with solutions.

Day 0

**6.30pm SOCIAL: Online meet-up & Quiz **

Day 1

Please note 9.00 Start

• 09:00 - 09:40; Welcome & Introduction to Functional Genomics (Mark & Rory)
• 09:40 - 12:30; Data Processing for Next Generation Sequencing (Joanna & Shoko)
  • Introduction to next generation sequencing
  • A brief Introduction to genomic file formats
  • Quality control and artefact removal
  • Practical - Learn to use FastQC and Cutadapt on a sample dataset
  • Short Read alignment and quality control
  • Practical - Alignment to reference genomes using BWA and STAR

• 12:30 - 13:30; LUNCH BREAK

• 13:30 - 17:00; Bulk RNAseq (Ash, Abbi & Chandu)
  • Introduction to RNAseq Analysis in R
  • RNA-seq Pre-processing

Day 2

• 09:30 - 17:00; Bulk RNAseq Continued (Ash, Dom & Chandu)
  • Statistical Analysis of Bulk RNAseq Data (Dom)
  • Experimental Design of Bulk RNAseq studies (Chandu)
  • Differential Expression for RNA-seq (Ash)
• 12:30 - 13:30; LUNCH

Day 3

• 09:30 - 12:30; Bulk RNAseq (cont.) (Ash & Abi)
  • Annotation and Visualisation of RNA-seq results (Abbi)
  • Gene-set testing (Ash)

• 12:30 - 13:30; LUNCH BREAK

• 13:30 - 17:00; Single Cell RNAseq (Stephane, & Kasia)
  • scRNA-seq - introduction, inc design
  • scRNA-seq - preprocessing, inc cell calling
  • scRNA-seq - normalisation, visualisation, batch correction

**6pm SOCIAL: Zoom Talk: “Perspectives in AI for Cancer Bioinformatics by Rory Stark”. **

—- Weekend —-

Day 4

• 09:30 - 17:00; Single Cell RNAseq (cont.) (Stephane & Zeynep)
  • scRNA-seq - feature selection and dimension reduction
  • scRNA-seq - clustering and marker gene detection
  • scRNA-seq - differential expression and differential abundance
• 12:30 - 13:30; LUNCH BREAK

Day 5

• 09:30 - 17:00; ChIPseq (Joanna & Shoko)
  • Introduction to ChIP-seq
  • Introduction to Peak Calling
  • Differential binding analysis
  • Quality control methods for ChIP-seq
  • Downstream analysis of ChIP-seq
  • Introduction to (epi)Genomic data integration
  • Chromatin accessibility and nucleosome occupancy with ATAC-seq
  • Useful software utilities for the analysis of genomic data
• 12:30 - 13:30; LUNCH BREAK

** End of CRUK CC Bioinformatics Summer School 2020**