49 materials found

Scientific topics: RNA-Seq 


High-throughput sequencing: Alignment and related topic

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

High-throughput sequencing: Alignment and related topic https://tess.elixir-europe.org/materials/high-throughput-sequencing-alignment-and-related-topic 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
Analysis of RNA-Seq Data

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

Analysis of RNA-Seq Data https://tess.elixir-europe.org/materials/analysis-of-rna-seq-data 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
CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems

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

CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems https://tess.elixir-europe.org/materials/crisprseek-design-of-target-specific-guide-rnas-in-crispr-cas9-genome-editing-systems 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
Visualization of Genomic Data

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

Visualization of Genomic Data https://tess.elixir-europe.org/materials/visualization-of-genomic-data 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
RNA-Seq 3: alternative exon usage

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 3: alternative exon usage https://tess.elixir-europe.org/materials/rna-seq-3-alternative-exon-usage 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
RNA-Seq 1: differential expression analysis - GLMs and testing

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 1: differential expression analysis - GLMs and testing https://tess.elixir-europe.org/materials/rna-seq-1-differential-expression-analysis-glms-and-testing 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
Work flows : RNA-Seq

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

Work flows : RNA-Seq https://tess.elixir-europe.org/materials/work-flows-rna-seq 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
Analysis of RNA-Seq using the DESeq2 package

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

Analysis of RNA-Seq using the DESeq2 package https://tess.elixir-europe.org/materials/analysis-of-rna-seq-using-the-deseq2-package 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
Counting reads for RNA-seq in Bioconductor

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

Counting reads for RNA-seq in Bioconductor https://tess.elixir-europe.org/materials/counting-reads-for-rna-seq-in-bioconductor 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
Introduction to RNA-Seq data analysis

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

Introduction to RNA-Seq data analysis https://tess.elixir-europe.org/materials/introduction-to-rna-seq-data-analysis 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
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 https://tess.elixir-europe.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
RNA-Seq

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 https://tess.elixir-europe.org/materials/rna-seq-387b1419-9068-4001-b32b-e43a513034c7 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
Differential Gene 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

Differential Gene Expression https://tess.elixir-europe.org/materials/differential-gene-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
Lecture: RNA-Seq data analysis and differential expression part II

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

Lecture: RNA-Seq data analysis and differential expression part II https://tess.elixir-europe.org/materials/lecture-rna-seq-data-analysis-and-differential-expression-part-ii 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
Lecture: RNA-Seq data analysis and differential expression part I

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

Lecture: RNA-Seq data analysis and differential expression part I https://tess.elixir-europe.org/materials/lecture-rna-seq-data-analysis-and-differential-expression-part-i 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
Workshop: RNASeq

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

Workshop: RNASeq https://tess.elixir-europe.org/materials/workshop-rnaseq 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
Supplement 2: RNA-Seq Statistical Issues

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

Supplement 2: RNA-Seq Statistical Issues https://tess.elixir-europe.org/materials/supplement-2-rna-seq-statistical-issues 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
Supplement 1: RNA-Seq Workflow

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

Supplement 1: RNA-Seq Workflow https://tess.elixir-europe.org/materials/supplement-1-rna-seq-workflow 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
RNA-Seq 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 Differential Expression https://tess.elixir-europe.org/materials/rna-seq-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
Analyzing splice events from RNA-seq data with SGSeq

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

Analyzing splice events from RNA-seq data with SGSeq https://tess.elixir-europe.org/materials/analyzing-splice-events-from-rna-seq-data-with-sgseq 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
Low-level exploratory data analysis and methods development for RNA-seq

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

Low-level exploratory data analysis and methods development for RNA-seq https://tess.elixir-europe.org/materials/low-level-exploratory-data-analysis-and-methods-development-for-rna-seq 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 https://tess.elixir-europe.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
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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
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
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
GATK Best practices for variant discovery

ÔÇïIn the course of this workshop, we highlight key functionalities such as  GVCF workflow for joint variant discovery in cohorts RNAseq-specific processing somatic variant discovery using MuTect2.  capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery the use...

Scientific topics: RNA-Seq

GATK Best practices for variant discovery https://tess.elixir-europe.org/materials/gatk-best-practices-for-variant-discovery ÔÇïIn the course of this workshop, we highlight key functionalities such as  GVCF workflow for joint variant discovery in cohorts RNAseq-specific processing somatic variant discovery using MuTect2.  capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery the use of pipelining tools to assemble and execute GATK workflows. RNA-Seq Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
Downstream processing of RNA-Seq data in GenePattern

- Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that interleave...

Scientific topics: RNA-Seq

Downstream processing of RNA-Seq data in GenePattern https://tess.elixir-europe.org/materials/downstream-processing-of-rna-seq-data-in-genepattern - Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place Summary The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists. 1. Running Analyses in GenePattern 2. Clustering 3. Prediction and Clasification 4. Working with analysis workflows: GenePattern pipelines 5. Working with Samples and Features 6. The GenePattern Notebook environment 7. Related tools: IGV, GSEA 8. Open Q&A The data files, slides and exercises will be made available after the workshop.   RNA-Seq Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09