News: Course - Genomics with R and Bioconductor - Berlin
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gravatar for carlopecoraro2
18 months ago by
carlopecoraro21.9k
Berlin
carlopecoraro21.9k wrote:

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Dear all,

we still have a few places left 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)


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

info@physalia-courses.org

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

Twitter: @physacourses

mobile: +49 17645230846

https://groups.google.com/forum/#!forum/physalia-courses

news bioconductor R • 517 views
ADD COMMENTlink written 18 months ago by carlopecoraro21.9k
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Hi,

Please switch to imgbb for image hosting - the website you're using is not compatible with biostars.

ADD REPLYlink written 18 months ago by _r_am32k
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