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10 materials found

Authors: Obi Griffith  or Charlotte Soneson  or St├®phane Plaisance 


Microbial genomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Microbiome

Microbial genomics https://tess.elixir-europe.org/materials/microbial-genomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Microbiome
Experimental design

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Experimental design

Experimental design https://tess.elixir-europe.org/materials/experimental-design Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Experimental design
New RNA-seq workflows

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: RNAseq

New RNA-seq workflows https://tess.elixir-europe.org/materials/new-rna-seq-workflows Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. RNAseq
Informatics for RNA-Seq Analysis 2018 Module 3-Expression and Differential Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2018 Module 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2018-module-3-expression-and-differential-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 3-Expression and Differential Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2017-module-3-expression-and-differential-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate Students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 9-Expression and Differential Expression

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 9-Expression and Differential Expression https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-9-expression-and-differential-expression Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Post-Doctoral Fellows Researchers Biologists, Genomicists, Computer Scientists
RNA-Seq analysis for differential expression

We first perform quality control of the sequence reads to detect biases or leftover adaptors. We then map the reads to the reference genome with use of a transcript database model. We perform a detailed QC analysis of the mapping results to again detect potential problems. The mapping data is...

Scientific topics: RNA-Seq, Gene expression

RNA-Seq analysis for differential expression https://tess.elixir-europe.org/materials/rna-seq-analysis-for-differential-expression We first perform quality control of the sequence reads to detect biases or leftover adaptors. We then map the reads to the reference genome with use of a transcript database model. We perform a detailed QC analysis of the mapping results to again detect potential problems. The mapping data is adjusted to compensate for artifacts like duplicates. The mappings are used to obtain transcript counts usable for differential expression. The count tables are merged and used to compute differential expression using several programs. We START a typical functional analysis of the obtained results similar to what is done for microarray data in order to exemplify handy tools and commercial alternatives. The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training. RNA-Seq Gene expression Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
Analysis of public microarray data using Genevestigator

The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression...

Scientific topics: Gene expression analysis, Gene expression, Biomarkers

Analysis of public microarray data using Genevestigator https://tess.elixir-europe.org/materials/analysis-of-public-microarray-data-using-genevestigator The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression information of many species in a user-friendly graphical way. The afternoon session will focus on the practical applications in a hands-on tutorial on Genevestigator followed by concrete examples of software that can be used to further interpret the results of your Genevestigator searches, like Ingenuity Pathway Analysis and DAVID. Finally, you will be able to work on the questions that you want to answer in your own research under the supervision of the trainer. Participants are therefore encouraged to submit a description of the objectives of the analysis they want to perform. Gene expression analysis Gene expression Biomarkers Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Analysis of public microarray data sets

This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session.

Scientific topics: Expression data visualisation

Analysis of public microarray data sets https://tess.elixir-europe.org/materials/analysis-of-public-microarray-data-sets This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session. Expression data visualisation Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Hands-on introduction to NGS variant analysis

This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.   This training does not cover all methods available today. It does...

Scientific topics: DNA

Hands-on introduction to NGS variant analysis https://tess.elixir-europe.org/materials/hands-on-introduction-to-ngs-variant-analysis This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.   This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs. DNA Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09