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Keywords: Experimental-design  or Unix 


Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R

An overview of Unix and R for bioinformatics

Keywords: Unix, R-programming

Resource type: Training materials

Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R https://tess.elixir-europe.org/materials/summer-school-2018-trainmalta-epigenomics-introduction-to-unix-and-r An overview of Unix and R for bioinformatics Luigi Grassi Unix, R-programming PhD students Life Science Researchers
An Introduction to Unix

Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this. This course provides an introduction to the concepts of unix and provides a...

Keywords: Unix, Babraham Institute

An Introduction to Unix https://tess.elixir-europe.org/materials/an-introduction-to-unix Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this. This course provides an introduction to the concepts of unix and provides a practical introduction to working in this environment. Internally we link this course to a more specific course illustrating the use of our internal cluster environment and this part of the course could be adapted for other sites with different compute infrastructure. Unix, Babraham Institute
UNIX Fundamentals

This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of...

Keywords: Problem based learning, Programming, Unix

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals-35adf82d-ae32-449d-9627-43b5d18da8cc This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of the course, participants are expected to be able to: Have some understanding on UNIX systems Navigate through the UNIX filesystem Execute and understand some UNIX process commands Correctly set file permissions Perform basic file management Participants are encouraged to follow the tutorial sections sequentially. The tutorial content is sometimes an oversimplification of the Truth - yes, we know! Due to the diversity of computer systems, we will just assume that participants do have access to a terminal. For help, please contact your IT support - or a good friend!Authors are affiliated to the SIB Swiss Institute of Bioinformatics: Vassilios IoannidisWith some content provided by Frédéric Schütz, Volker Flegel and Heinz StockingerContent integration by Grégoire Rossier and Vassilios Ioannidis Problem based learning, Programming, Unix Bench biologists Clinical Scientists Graduate Students beginner bioinformaticians biocurators 2014-01-13 2017-10-09
ChIP-seq analysis using R - Experimental design and peak calling.

This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling.

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Visualisation

ChIP-seq analysis using R - Experimental design and peak calling. https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-experimental-design-and-peak-calling-cfd4c18f-6c86-45ae-ab0b-630422c76af6 This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling. ChIP-Seq, Experimental-design, Peak-calling, Visualisation
ChIP-seq analysis using R

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a...

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming

ChIP-seq analysis using R https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-5049bc9c-9bbb-4a6b-9244-37ed3980da0e ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a theoretical background and the means to perform peak calling and differential binding analysis. ChIP-Seq, Experimental-design, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming
UNIX command line and scripting

The first part of this course introduces the UNIX command line on a Linux or Mac. The second part provides a basic introduction to string searches and scripting with AWK and BASH.

Keywords: Awk, Bash, Unix

UNIX command line and scripting https://tess.elixir-europe.org/materials/unix-command-line-and-scripting The first part of this course introduces the UNIX command line on a Linux or Mac. The second part provides a basic introduction to string searches and scripting with AWK and BASH. Awk, Bash, Unix 2016-04-21 2017-10-09
ChIP-seq analysis using R - Experimental design and peak calling.

This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling.

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Visualisation

ChIP-seq analysis using R - Experimental design and peak calling. https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-experimental-design-and-peak-calling This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling. ChIP-Seq, Experimental-design, Peak-calling, Visualisation
ChIP-seq analysis using R - Quality Control

This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - Quality Control https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-quality-control This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
ChIP-seq analysis using R - File formats and QC

This lecture introduces the file formats of sequencing data before alignment and covers the general quality control of sequencing data focussing on RNA-Seq and ChIP-Seq.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - File formats and QC https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-file-formats-and-qc This lecture introduces the file formats of sequencing data before alignment and covers the general quality control of sequencing data focussing on RNA-Seq and ChIP-Seq. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
ChIP-seq analysis using R - Quality Control Walkthrough

This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - Quality Control Walkthrough https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-quality-control-walkthrough This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
An Introduction to Unix, Perl and Python

This  course provides an introduction to Unix, Perl and Python. In addition to lecture material (in the form of slides), there are exercises, answers to the exercises and pointers to addition resources.

Keywords: Perl, Python, Unix

An Introduction to Unix, Perl and Python https://tess.elixir-europe.org/materials/an-introduction-to-unix-perl-and-python This  course provides an introduction to Unix, Perl and Python. In addition to lecture material (in the form of slides), there are exercises, answers to the exercises and pointers to addition resources. Perl, Python, Unix Bench biologists 2013-07-28 2017-10-09
ChIP-Seq

No description available

Keywords: ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation

ChIP-Seq https://tess.elixir-europe.org/materials/chip-seq No description available ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation
Prerequisite

No description available

Scientific topics: Statistics and probability

Keywords: Unix, Linux, R-programming, Statistics

Prerequisite https://tess.elixir-europe.org/materials/prerequisite No description available Statistics and probability Unix, Linux, R-programming, Statistics
ChIP-seq analysis using R

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a...

Keywords: ChIP-Seq, Experimental-design, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation

ChIP-seq analysis using R https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a theoretical background and the means to perform peak calling and differential binding analysis. ChIP-Seq, Experimental-design, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation