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20 materials found

Keywords: Exploratory-analysis  or John Innes Centre 


Introduction to Linux: The operating system for bioinformatics

Linux is the operating system of high performance clusters and supercomputers all over the world. Learning to use Linux is a key part of making use of cutting edge bioinformatics tools. This course provides an extensive introduction to Linux, covering both basic and advanced use.

Keywords: John Innes Centre, JIC

Introduction to Linux: The operating system for bioinformatics https://tess.elixir-europe.org/materials/introduction-to-linux-the-operating-system-for-bioinformatics Linux is the operating system of high performance clusters and supercomputers all over the world. Learning to use Linux is a key part of making use of cutting edge bioinformatics tools. This course provides an extensive introduction to Linux, covering both basic and advanced use. John Innes Centre, JIC Any students, postdocs or RAs who have an interest in bioinformatics and who intend to conduct their own analyses on a Linux platform. Those intending to register for the upcoming Introduction to HPC course are very strongly encouraged to attend this short (two morning) course and it should be seen as a prerequisite for later courses to be offered on ChIP-Seq analysis and command line/Galaxy implementations of NGS workflows.
Python for Biologists: Programming for Scientific Computing

Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.

Scientific topics: Software engineering

Keywords: Python for Biologists, John Innes Centre, JIC

Python for Biologists: Programming for Scientific Computing https://tess.elixir-europe.org/materials/python-for-biologists-programming-for-scientific-computing Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences. Software engineering Python for Biologists, John Innes Centre, JIC For beginners interested in using Python to solve problems in Biology.
Introduction to R: A software environment for statistical computing

R is a free software environment for statistical computing and graphics. It is widely used in scientific data analysis. R is a great tool for biologists, since it provides cutting edge statistical techniques, excellent graph and figure plotting capabilities and bioinformatics tools all in one...

Scientific topics: Software engineering, Statistics and probability

Keywords: John Innes Centre, JIC

Introduction to R: A software environment for statistical computing https://tess.elixir-europe.org/materials/introduction-to-r-a-software-environment-for-statistical-computing R is a free software environment for statistical computing and graphics. It is widely used in scientific data analysis. R is a great tool for biologists, since it provides cutting edge statistical techniques, excellent graph and figure plotting capabilities and bioinformatics tools all in one package. Software engineering Statistics and probability John Innes Centre, JIC Any students, postdocs or RAs who have an interest in bioinformatics and who intend to carry out statistical analysis of their experimental data using R. This two day course is planned to be a very gentle introduction to the very basic concepts of R.
Introduction to Perl: Programming for bioinformatics

Perl is a powerful programming language that is heavily used in the bioinformatics community. This course will provide a full introduction to the basics of Perl, as well as how to carry out common bioinformatics tasks.

Scientific topics: Software engineering

Keywords: perl, John Innes Centre, JIC

Introduction to Perl: Programming for bioinformatics https://tess.elixir-europe.org/materials/introduction-to-perl Perl is a powerful programming language that is heavily used in the bioinformatics community. This course will provide a full introduction to the basics of Perl, as well as how to carry out common bioinformatics tasks. Software engineering perl, John Innes Centre, JIC Any students, postdocs or RAs who have an interest in programming and who intend to carry out computational analysis of their experimental data. Perl is often used for preparing input files for more specialized software such as R, and also to post-process the output from R and various other bioinformatics tools. It is a glue language allowing you to build pipelines of analyses of arbitrary complexity. This two day course is planned to be a gentle introduction to the basic concepts of Perl and will also introduce you to the BioPerl library of modules.
Computational Bioimaging: From images to data

Bioimaging is a rich source of data in biology. However, quantifying those data requires a strong understanding of the correct computational techniques. This course provides an introduction to those techniques, with a focus on transforming raw data from microscopes into meaningful information...

Scientific topics: Imaging, Biological imaging

Keywords: John Innes Centre, JIC

Computational Bioimaging: From images to data https://tess.elixir-europe.org/materials/computational-bioimaging Bioimaging is a rich source of data in biology. However, quantifying those data requires a strong understanding of the correct computational techniques. This course provides an introduction to those techniques, with a focus on transforming raw data from microscopes into meaningful information about the systems studied. Imaging Biological imaging John Innes Centre, JIC Those interesting in exploring the data contained in their microscopy images, or those planning microscopy as part of their research programme
Introduction to RNA-Seq Using Galaxy: Studying the transcriptome

RNA-Seq provides a method for understanding transcriptional dynamics in biological systems. It has immense power to enhance our understanding of those systems, but carrying out RNA-Seq analysis requires use of multiple related software packages. This hands-on course provides experience in using...

Scientific topics: RNA, RNA-Seq

Keywords: John Innes Centre, JIC

Introduction to RNA-Seq Using Galaxy: Studying the transcriptome https://tess.elixir-europe.org/materials/introduction-to-rna-seq-using-galaxy RNA-Seq provides a method for understanding transcriptional dynamics in biological systems. It has immense power to enhance our understanding of those systems, but carrying out RNA-Seq analysis requires use of multiple related software packages. This hands-on course provides experience in using these packages as part of an RNA-Seq analysis pipeline. RNA RNA-Seq John Innes Centre, JIC Students, postdocs or RAs who have an interest in bioinformatics and who intend to conduct RNA-Seq analysis on a Galaxy platform
Galaxy for NGS analysis: A web-based platform for data intensive biological research

Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The workbench interface is...

Scientific topics: Workflows, High-throughput sequencing, Nucleic acid sequence analysis, Bioinformatics

Keywords: John Innes Centre, JIC

Galaxy for NGS analysis: A web-based platform for data intensive biological research https://tess.elixir-europe.org/materials/galaxy-for-ngs-analysis Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The workbench interface is simple and intuitive, supports collaboration and integrates data and analysis tools together in a single place. Workflows High-throughput sequencing Nucleic acid sequence analysis Bioinformatics John Innes Centre, JIC
RNA-seq module Frederik Coppens

Material concerning RNA-seq analysis, with an emphasis on the statistical aspects.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens-4a328fa8-0bef-471c-84e4-b0d89d216128 Material concerning RNA-seq analysis, with an emphasis on the statistical aspects. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Variant-calling

No description available

Keywords: Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF

Variant-calling https://tess.elixir-europe.org/materials/variant-calling No description available Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
Day 4 - RNA-Seq Analysis

Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation.

Keywords: Exploratory-analysis, Differential-expression, Statistical-model, Annotation

Day 4 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-4-rna-seq-analysis Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation. Exploratory-analysis, Differential-expression, Statistical-model, Annotation
Statistics and RNA-Seq

This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

Statistics and RNA-Seq https://tess.elixir-europe.org/materials/statistics-and-rna-seq This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Material for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis.

Scientific topics: RNA-Seq

Keywords: RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Material for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/material-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. RNA-Seq RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
Material provided by Charlotte Soneson

This folder contains material provided by Charlotte Soneson. The following material is included:

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis

Material provided by Charlotte Soneson https://tess.elixir-europe.org/materials/material-provided-by-charlotte-soneson This folder contains material provided by Charlotte Soneson. The following material is included: RNA-Seq RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis
RNA-seq module Eija Korpelainen

All material concerning RNA-seq data analysis with Chipster

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Eija Korpelainen https://tess.elixir-europe.org/materials/rna-seq-module-eija-korpelainen All material concerning RNA-seq data analysis with Chipster FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exercises for the course RNA-seq data analysis with Chipster

This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Day 2 - RNA-Seq Analysis

Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser.

Keywords: Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing

Day 2 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-2-rna-seq-analysis Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser. Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing
Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exploratory analysis and downstream analysis

This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods...

Keywords: Statistical-model, Exploratory-analysis

Exploratory analysis and downstream analysis https://tess.elixir-europe.org/materials/exploratory-analysis-and-downstream-analysis This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods developed (e.g.) for microarray data. Statistical-model, Exploratory-analysis