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25 materials found

Keywords: Exploratory-analysis  or Gene Expression 


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
Functional genomics (III): Submitting your data and functional genomics databases

Functional genomics (III): Submitting your data and functional genomics databases from http://www.ebi.ac.uk/training/online/course/functional-genomics-iii-submitting-your-data-and-f.

Keywords: Gene Expression

Functional genomics (III): Submitting your data and functional genomics databases https://tess.elixir-europe.org/materials/functional-genomics-iii-submitting-your-data-and-functional-genomics-databases Functional genomics (III): Submitting your data and functional genomics databases from http://www.ebi.ac.uk/training/online/course/functional-genomics-iii-submitting-your-data-and-f. Gene Expression 2016-06-14
Functional genomics (II): Common technologies and data analysis methods

Functional genomics (II): Common technologies and data analysis methods from http://www.ebi.ac.uk/training/online/course/functional-genomics-ii-common-technologies-and-dat.

Keywords: Gene Expression

Functional genomics (II): Common technologies and data analysis methods https://tess.elixir-europe.org/materials/functional-genomics-ii-common-technologies-and-data-analysis-methods Functional genomics (II): Common technologies and data analysis methods from http://www.ebi.ac.uk/training/online/course/functional-genomics-ii-common-technologies-and-dat. Gene Expression 2016-06-14
Functional genomics (I): Introduction and designing experiments

Functional genomics (I): Introduction and designing experiments from http://www.ebi.ac.uk/training/online/course/functional-genomics-i-introduction-and-designing-e.

Keywords: Gene Expression

Functional genomics (I): Introduction and designing experiments https://tess.elixir-europe.org/materials/functional-genomics-i-introduction-and-designing-experiments Functional genomics (I): Introduction and designing experiments from http://www.ebi.ac.uk/training/online/course/functional-genomics-i-introduction-and-designing-e. Gene Expression 2016-06-14
ArrayExpress: Discover functional genomics data quickly and easily

ArrayExpress: Discover functional genomics data quickly and easily from http://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui.

Keywords: Gene Expression

ArrayExpress: Discover functional genomics data quickly and easily https://tess.elixir-europe.org/materials/arrayexpress-discover-functional-genomics-data-quickly-and-easily ArrayExpress: Discover functional genomics data quickly and easily from http://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui. Gene Expression 2016-06-14
Functional genomics: An introduction to EMBL-EBI resources

Functional genomics: An introduction to EMBL-EBI resources from http://www.ebi.ac.uk/training/online/course/functional-genomics-introduction-embl-ebi-resource-1.

Keywords: Gene Expression

Functional genomics: An introduction to EMBL-EBI resources https://tess.elixir-europe.org/materials/functional-genomics-an-introduction-to-embl-ebi-resources Functional genomics: An introduction to EMBL-EBI resources from http://www.ebi.ac.uk/training/online/course/functional-genomics-introduction-embl-ebi-resource-1. Gene Expression 2016-06-14
Expression Atlas: Quick tour

Expression Atlas: Quick tour from http://www.ebi.ac.uk/training/online/course/expression-atlas-quick-tour-0.

Keywords: Gene Expression

Expression Atlas: Quick tour https://tess.elixir-europe.org/materials/expression-atlas-quick-tour Expression Atlas: Quick tour from http://www.ebi.ac.uk/training/online/course/expression-atlas-quick-tour-0. Gene Expression 2016-06-14
EMBO Practical Course on Analysis of High-Throughput Sequencing Data

EMBO Practical Course on Analysis of High-Throughput Sequencing Data from http://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-high-throughput-seq.

Keywords: Gene Expression

EMBO Practical Course on Analysis of High-Throughput Sequencing Data https://tess.elixir-europe.org/materials/embo-practical-course-on-analysis-of-high-throughput-sequencing-data EMBO Practical Course on Analysis of High-Throughput Sequencing Data from http://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-high-throughput-seq. Gene Expression 2016-06-14
EBI: Next Generation Sequencing Practical Course

EBI: Next Generation Sequencing Practical Course from http://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course.

Scientific topics: Sequencing

Keywords: DNA RNA, Gene Expression

EBI: Next Generation Sequencing Practical Course https://tess.elixir-europe.org/materials/ebi-next-generation-sequencing-practical-course EBI: Next Generation Sequencing Practical Course from http://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course. Sequencing DNA RNA, Gene Expression 2016-06-14
diXa data warehouse: Exploring data from toxicogenomics studies

diXa data warehouse: Exploring data from toxicogenomics studies from http://www.ebi.ac.uk/training/online/course/dixa-data-warehouse-exploring-data-toxicogenomics.

Keywords: Gene Expression, Ontologies, Chemical biology

diXa data warehouse: Exploring data from toxicogenomics studies https://tess.elixir-europe.org/materials/dixa-data-warehouse-exploring-data-from-toxicogenomics-studies diXa data warehouse: Exploring data from toxicogenomics studies from http://www.ebi.ac.uk/training/online/course/dixa-data-warehouse-exploring-data-toxicogenomics. Gene Expression, Ontologies, Chemical biology 2016-06-14
BioSamples: Quick tour

BioSamples: Quick tour from http://www.ebi.ac.uk/training/online/course/biosamples-quick-tour.

Keywords: DNA RNA, Gene Expression, Ontologies, Proteins

BioSamples: Quick tour https://tess.elixir-europe.org/materials/biosamples-quick-tour BioSamples: Quick tour from http://www.ebi.ac.uk/training/online/course/biosamples-quick-tour. DNA RNA, Gene Expression, Ontologies, Proteins 2016-06-14
BioSamples Database RDF: webinar

BioSamples Database RDF: webinar from http://www.ebi.ac.uk/training/online/course/biosamples-database-rdf-webinar.

Keywords: DNA RNA, Gene Expression, Ontologies, Proteins

BioSamples Database RDF: webinar https://tess.elixir-europe.org/materials/biosamples-database-rdf-webinar BioSamples Database RDF: webinar from http://www.ebi.ac.uk/training/online/course/biosamples-database-rdf-webinar. DNA RNA, Gene Expression, Ontologies, Proteins 2016-06-14
ArrayExpress: Quick tour

This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress. This course was updated in December 2015. An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI...

Scientific topics: Functional genomics, Gene expression and microarray, Gene expression

Keywords: Gene Expression

ArrayExpress: Quick tour https://tess.elixir-europe.org/materials/arrayexpress-quick-tour This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress. This course was updated in December 2015. An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI resources before taking this course. Functional genomics Gene expression and microarray Gene expression Gene Expression Beginners 2016-06-14
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