ChIP-Seq Analysis with Galaxy

10.12.2012

Introduction to Galaxy with a focus on ChIP-Seq data.

Slides:

  1. Introduction
  2. Quality Control on NGS Data
  3. File Formats pt1 (NGS Data) 
  4. File Formats pt2 (Genomic Features)
  5. Peak Calling + Practical Part
  6. Putative Binding Motif Discovery
  7. (watch out for more)

 

Addendum:

Coverage vs. expected duplicates in the human genome

 

DATE Dec 10 + 11, 2012
TIME 9:00 - 12:30 
LOCATION GMI Orange Room

Bettina Grün's photo

R for Biologists Course #2

22.05.2012

The second "R for Biologists" course will be held on the 2nd, 3rd and 4th of July. The course instructor is again Bettina Grün (JKU Linz).

Agenda:

While the main topics discussed in the course are fixed, please note that the details are subject to change.

Monday, 2nd July 2012. Venue: VBC2 seminar room (ground floor)

09:00 - 10:30 Introduction to R

10:30 - 11:00 Coffee break

11:00 - 12:30 Descriptive Statistics

Tuesday, 3rd July 2012. Venue: VBC2 seminar room (ground floor)

09:00 - 10:30 Data Import and Manipulation

10:30 - 11:00 Coffee break

11:00 - 12:30 Graphics in R

Wednesday, 4th July 2012. Venue: VBC 2 seminar room (ground floor)

13:30 - 15:00 Uni- and bivariate Inference

15:00 - 15:30 Coffee break

15:30 - 17:00 Linear Regression

Detailed Program:

introduction to R

  • What is R/S?
  • The language R
    • R as a pocket calculator
    • Important operators
    • Variables
    • Functions
  • Data types in R
    • Vectors: numeric, character, logical; access, names, conversion
    • Factors, ordered factors
    • Data frames
    • Missing values, special values
    • Matrices
  • Help and hints

Descriptive statistics

Numerical description/characterization and visualization of

one and two categorical variablesone and two numerical variablesone categorical and one numerical variable

Data import and manipulation

  • Import from text files, Excel sheets, output from other statistical packages
  • Manipulating data frames
  • Manipulating variables
  • apply and friends

Graphics in R

  • Graphics devices
  • Basic graphics: high-level and low-leve plots, parameters, annotation
  • Trellis plots with lattice

Uni- and bivariate inference

Suitable test procedures for:

  • one and two categorical variables
  • one and two numerical variables
  • one categorical and one numerical variable

linear regression

  • Linear models and ANOVA
  • Model specification via formulas
  • Fitted models

Genome Browser in Galaxy

01.08.2011

Galaxy is a workflow tool to analyse bioinformatic data focusing on simplicity and reproducibility. Now it includes a visualization plugin to view genomic data as we continue to offer your data ready to use in galaxy this enables comparison between analytic steps you performed in galaxy without the need to export data and import it into a genome browser.

DATE Thursday August 11th 2011
TIME 15:00
LOCATION IMP Seminar Room 3

Usermeeting with Focus on RNA

28.07.2011

Roger talks about his experiences with RNA-seq

DATE Thursday March 10th 2011
TIME 15:00
SPEAKER
LOCATION IMP Seminar Room

Usermeeting focusing on Chip-Seq

28.07.2011

 

 

DATE Thursday March 17th 2011
TIME 15:00
SPEAKER ...
LOCATION IMP Seminar Room

 

Galaxy Introduction (beta)

28.07.2011

 

TITLE: Galaxy Introduction 
DATE
Thursday March 24th 2011
TIME 14:00
LOCATION IMP Seminar Room

Campus Science Support
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Austria

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