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13 materials found

Scientific topics: Toxicology  or RNA-Seq 


Tutorial on CARNIVAL

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL

Scientific topics: RNA-Seq, Omics, Gene expression, Molecular interactions, pathways and networks

Operations: RNA-Seq analysis, Network analysis

Keywords: HPC, Signaling, RNAseq, transcriptomics

Resource type: Tutorial

Tutorial on CARNIVAL http://tess.elixir-uk.org/materials/tutorial-on-carnival This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL RNA-Seq Omics Gene expression Molecular interactions, pathways and networks HPC, Signaling, RNAseq, transcriptomics
A Tidy Transcriptomics introduction to RNA-Seq analyses

This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.

Scientific topics: RNA-Seq

Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics

Resource type: Tutorial

A Tidy Transcriptomics introduction to RNA-Seq analyses http://tess.elixir-uk.org/materials/a-tidy-transcriptomics-introduction-to-rna-seq-analyses This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages. RNA-Seq Differential Expression, Gene Expression, RNA-seq, Transcriptomics Biologists
OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

OpenRiskNet: Ontology Walkthrough and Workshop http://tess.elixir-uk.org/materials/openrisknet-ontology-walkthrough-and-workshop Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology. Ontology and terminology Toxicology Biologists bioinformaticians Chemists
Detecting differentially expressed genes with RNA-seq 11.9.2019

This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and...

Scientific topics: RNA-Seq

Detecting differentially expressed genes with RNA-seq 11.9.2019 http://tess.elixir-uk.org/materials/detecting-differentially-expressed-genes-with-rna-seq This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the workshop is thus suitable for everybody. RNA-Seq
Bioinformatics Summer School 2019

This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are...

Scientific topics: Statistics and probability, Omics, RNA-Seq, Proteomics

Operations: Data handling

Bioinformatics Summer School 2019 http://tess.elixir-uk.org/materials/bioinformatics-summer-school-2019 This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are familiar with omics experimental technologies and their applications in biology, have had some exposure with R, and who want to learn or expand their bioinformatics skills. Martin Morgan Laurent Gatto Janick Mathys Lieven Clement Charlotte Soneson Koen Van den Berge Oliver Crook Statistics and probability Omics RNA-Seq Proteomics PhD students
Single cell RNA-seq data analysis with R

This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with R http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r-26ec3ec0-8f43-47db-9788-7f8f63eb447b This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE project. Note: You can find all the course material including the R code and data files in the course [GitHub](https://github.com/NBISweden/excelerate-scRNAseq) repository, and the lecture videos are available as a [YouTube playlist](https://www.youtube.com/playlist?list=PLjiXAZO27elC_xnk7gVNM85I2IQl5BEJN). Eija Korpelainen @eija, ekorpelainen@gmail.com RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
RNA-Seq Lab: Workflow -- gene-level exploratory analysis and differential expression

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...

Scientific topics: RNA-Seq

RNA-Seq Lab: Workflow -- gene-level exploratory analysis and differential expression http://tess.elixir-uk.org/materials/rna-seq-lab-workflow-gene-level-exploratory-analysis-and-differential-expression 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. RNA-Seq
Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with R http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
Adding nanomaterial data

This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.

Scientific topics: Database management, Toxicology

Keywords: nanotoxicology, enanomapper, resource description framework, ontology

Resource type: Tutorial

Adding nanomaterial data http://tess.elixir-uk.org/materials/adding-nanomaterial-data This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format. Database management Toxicology nanotoxicology, enanomapper, resource description framework, ontology programmers data entering
Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

Scientific topics: RNA-Seq

Resource type: course materials, Video

Virus detection using small RNA-seq http://tess.elixir-uk.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
RNA-seq data analysis

This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...

Scientific topics: RNA-Seq

Resource type: course materials, Video

RNA-seq data analysis http://tess.elixir-uk.org/materials/rna-seq-data-analysis-with-chipster This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
RNA-Seq Analysis

This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of RNA-Seq data. The course starts with a comprehensive lecture covering the theory of RNA-Seq data generation and...

Scientific topics: RNA-Seq

RNA-Seq Analysis http://tess.elixir-uk.org/materials/rna-seq-analysis-d7e62d71-a253-4168-8b5d-6838a2384978 This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of RNA-Seq data. The course starts with a comprehensive lecture covering the theory of RNA-Seq data generation and analysis and is then followed by a long hands-on practical session which runs though the entire RNA-Seq analysis pipeline from raw fastq files to a list of differentially expressed candidate genes. RNA-Seq