This lecture introduces the basic concepts of ChIP-seq data analysis. Various approaches for quality control are discussed, as well as data normalization and peak calling.  

 

The bioconductor authoring tool links the journal’s manuscript management system with the Bioconductor nightly build system, thus enabling “continuous Integration”, automated quality control and guaranteed workflow functionality even as underlying resources and tools evolve. A package and tutorial publication are underway, and we have actively helped several authors from the community with workflow authoring.

Homepage

https://bioconductor.org/packages/BiocWorkflowTools/

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Mike Smith

Type of Material: Publishing channel in F1000

The F1000Research Channel for R/Bioconductor-based workflows was established with support from HD-HuB personnel. These workflows are peer-reviewed academic articles, which increases quality and offers an additional incentive for their authors. The channel is well accepted by the international bioinformatics community.

https://f1000research.com/channels/bioconductor

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Mike Smith

Type of Material: Coursebook of Bioimage Analysis Course

This course material intends to provide a basic introduction into the KNIME (image) data analytics functionalities and the concept of integrative data analysis. Apart from the powerful tools inherited by KNIME itself, one of the basic ideas behind KNIME is to integrate established and commonly used software (like the ImageJ framework for image processing), thus enabling to make use of the power of the KNIME data analytics after having processed the original input raw data (like bioimage raw data in case of image processing).

Contact

Dr. Manuel Gunkel

Open Coursebook

Type of Material: Lecture Slides (2017)

This lecture introduces the basic concepts of ChIP-seq data analysis. Various approaches for quality control are discussed, as well as data normalization and peak calling.These slides are supplementary material from the video lecture "An Introduction to ChipSeq Analysis" by Dr. Carl Herrmann available here.

Contact:

Carl Herrmann (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Open Slides

Type of Material: exercises, handouts, scripting data, solutions

Linux is an operating system with a powerful command line interface that is widely used for biological data analysis and in server and cluster systems. A knowledge and understanding of how to interact effectively with the command line is essential when using many popular bioinformatics software packages, efficiently performing repetitive computational tasks, and working in high-performance computing cluster environments.

This course aims to teach basic commands and shell scripting to the life-scientists who wish to carry out repeated tasks to deal with biological data.

Here you can find a copious collection of Course Materials.

Contact

Frank Thommen

Open Course Material

Type of Material: Lecture Slides (2017)

These slides describe in detail two databases, GenomeRNAi and GenomeCRISPR, for phenotypes discovered in functional high‐throughput screens. The slides guide through the user interfaces of both database websites highlighting their functionality in the context of specific biological queries. They discuss the processes of both data curation and integration with external resources. Finally the identification of genetic interactions in cancer cells serves as an example of how database context can be mined to generate new biological findings.

Contact

Benedikt Rauscher

Open Slides

Type of Material: exercices, handouts, scripting data, solutions, Jupyter notebooks

The aim of Software Carpentry is to enable researchers to be more productive while
producing work of higher quality. This online material teaches the key skills
required to practise robust computational science effectively and efficiently, and
provide an overview of some of the tools and resources available for modern
computational biology.

The material contains introductions for novices to the Unix Shell, Python and git.

Here you can find a copious collection of course materials for the Software Carpentry workshop taken place in Berlin 2017-06-19/2017-06-20

Here you can find a copious collection of course materials for the Software Carpentry workshop taken place in Würzburg 2017-09-04/2017-09-05

Contact:

Dr. Georg Zeller

Malvika Sharan

Toby Hodges (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Type of Material: Lecture Slides (2017)

These slides theoretically explain how to make your data analysis workflows more portable and interoperable with the Common Workflow Language (CWL*)

* “CWL is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high-performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL is developed by an informal, multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is on Github and we follow the Open-Stand.org principles for collaborative open standards development.” (Source).

Contact:

Dr. Georg Zeller

Malvika Sharan

Toby Hodges (This email address is being protected from spambots. You need JavaScript enabled to view it.)

 Open Slides

Joomla templates by a4joomla