Course -Genomics with R and Bioconductor - Berlin 16-20 September 2019

[Physalia-courses]

Dear all,

still a few places on our course " Genomics with R and Bioconductor"

Where: Free University (FU) Berlin (Germany)

When: 16-20 September 2019

Instructor: Dr. Ludwig Geistlinger - CUNY Graduate School of Public Health and Health Policy, New York (USA)

Registration deadline: August 20th

Course:

This course will provide biologists and bioinformaticians with practical statistical analysis skills to perform rigorous analysis of high-throughput genomic data. The course assumes basic familiarity with genomics and with R programming, but does not assume prior statistical training. It covers the statistical concepts necessary to design experiments and analyze high-throughput data generated by next-generation sequencing, including: exploratory data analysis, principal components analysis, clustering, differential expression, and gene set analysis.

Programme:

Session 1 – Introduction

Monday - 09:30 to 17:30

Lecture 1: Data distributions

random variables
distributions
population and samples

Hands-On 1: Introduction to R

Lecture 2: Creating high-quality graphics in R

Visualizing data in 1D, 2D & more than two dimensions
Heatmaps
Data transformations

Hands-On 2: Graphics with base R and ggplot2

Session 2 – Hypothesis testing

Tuesday - 09:30 to 17:30

Lecture 1: Hypothesis testing theory

type I and II error and power
multiple hypothesis testing: false discovery rate, familywise error rate
exploratory data analysis (EDA)

Hands-On 1: Standard tests & EDA

Lecture 2: Hypothesis testing in practice

hypothesis tests for categorical variables (chi-square, Fisher's exact)
Monte Carlo simulation
Permutation tests

Hands-On 2: Permutation tests

Session 3 - Bioconductor

Wednesday – Classes from 09:30 to 17:30

Lecture 1: Introduction to Bioconductor

Incorporating Bioconductor in your data analysis
ExpressionSet / SummarizedExperiment
Annotation resources

Hands-On 1: Leveraging Bioconductor annotation resources

Lecture 2: Genomic intervals

Introduction to genomic region algebra
Basic operations: construction, intra- and inter-region operations
Finding overlaps

Hands-On 2: Solving common bioinformatic challenges with GenomicRanges

Session 4 - Next-generation sequencing data

Thursday - 09:30 to 17:30

Lecture 1: High-throughput count data

Characteristics of count data
Exploring count data
Modeling count data

Hands-On 1: Analyzing next-generation sequencing data

Lecture 2: Clustering and Principal Components Analysis

Measures of similarity
Hierarchical clustering
Dimension reduction
Principal components analysis (PCA)

Hands-On 2: Clustering & PCA

Session 5 - Differential expression and gene set analysis

Friday - 09:30 to 17:30

Lecture 1 - Differential expression analysis

Normalization
Experimental designs
Generalized linear models

Lab 1: Performing differential expression analysis with DESeq2

Lecture 2 - Gene set analysis

A primer on terminology, existing methods & statistical theory
GO/KEGG overrepresentation analysis
Functional class scoring & permutation testing
Network-based enrichment analysis

Lab 2: Performing gene set enrichment analysis with the EnrichmentBrowser

For the full list of our courses and Workshops, please see: https://www.physalia-courses.org/courses-workshops

Should you have any questions, please feel free to contact us

Thanks and best regards,

Carlo

Carlo Pecoraro, Ph.D

Physalia-courses DIRECTOR

[email protected]

http://www.physalia-courses.org/

Twitter: @physacourses

mobile: +49 17645230846

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