19 materials found

Keywords: Differential-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
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
Introduction to RNA-seq analysis 2014

This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species.

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

Introduction to RNA-seq analysis 2014 https://tess.elixir-europe.org/materials/introduction-to-rna-seq-analysis-2014 This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
RNA-seq training PSB 2013

This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage...

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

RNA-seq training PSB 2013 https://tess.elixir-europe.org/materials/rna-seq-training-psb-2013 This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage and sequencing mode is touched upon as well as the effect on your analysis of divergence of your genotype compared to the reference. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
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
Nicolas Delhomme and Bastian Schiffthaler

This merely lists the various courses at which we taught RNA-Seq data

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Nicolas Delhomme and Bastian Schiffthaler https://tess.elixir-europe.org/materials/nicolas-delhomme-and-bastian-schiffthaler This merely lists the various courses at which we taught RNA-Seq data RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
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
Differential expression analysis

This lecture covers the process from count matrix to statistical analysis results (differential expression). More specifically, it covers experimental design, normalization, statistical modeling and parameter estimation, multiple hypothesis testing and a more detailed look at some of the most...

Keywords: Differential-expression, Statistical-model

Differential expression analysis https://tess.elixir-europe.org/materials/differential-expression-analysis This lecture covers the process from count matrix to statistical analysis results (differential expression). More specifically, it covers experimental design, normalization, statistical modeling and parameter estimation, multiple hypothesis testing and a more detailed look at some of the most common differential expression methods as well as a comparison between them. Differential-expression, Statistical-model
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
Populus tremula shows no evidence of sexual dimorphism

**Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and...

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression

Populus tremula shows no evidence of sexual dimorphism https://tess.elixir-europe.org/materials/populus-tremula-shows-no-evidence-of-sexual-dimorphism **Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. The establishment of such sexual dimorphism would result in changes in gene expression patterns in non-floral organs. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression
Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material

Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and...

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material https://tess.elixir-europe.org/materials/nicolas-delhomme-bastian-schiffthaler-october-2014-embo-course-material Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and reproduces the Differential Expression analysis conducted in Robinson, Delhomme et al., 2014. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Differential expression analysis on the Robinson, Delhomme et al. dataset.

A differential expression analysis conducted on the **[Robinson, Delhomme et al., dataset](https://microasp.upsc.se/ngs_trainers/Materials/blob/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md)**. The dataset has 17 samples and 2 important meta-data: the...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, R-programming, Statistical-model

Differential expression analysis on the Robinson, Delhomme et al. dataset. https://tess.elixir-europe.org/materials/differential-expression-analysis-on-the-robinson-delhomme-et-al-dataset A differential expression analysis conducted on the **[Robinson, Delhomme et al., dataset](https://microasp.upsc.se/ngs_trainers/Materials/blob/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md)**. The dataset has 17 samples and 2 important meta-data: the sample sex and year of collection. The goal is to test whether genes are involved in different processes based on the sex of the tree; _i.e._ is there a sexual dimorphism in _Populus tremula_ trees. It has indeed been hypothesized that male tree should be taller so as to spread their pollen further, whereas female would be more resistant to pests and diseases. The existing literature is contradictory, however it resulted from studies where plants were grown in controlled environment. In the present dataset, plant samples were collected in the wild, at a 2 years interval. The latter is a very important factor in the analysis as the 'year effect' is a strong confounding factor that hides the 'sex effect'. The present tutorial, hence, introduces a differential-expression analysis, but goes further by adressing confounding factors and how to _block_ them in an analysis. It is a good dataset to remind trainees that they should always be critical towards the conclusion they draw from their data. RNA-Seq RNA-Seq, Differential-expression, R-programming, Statistical-model
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
Introduction to NGS and RNA-seq

No description available

Keywords: HTS-introduction, Data-format, Alignment, Differential-expression, Feature-summarisation, QC

Introduction to NGS and RNA-seq https://tess.elixir-europe.org/materials/introduction-to-ngs-and-rna-seq No description available HTS-introduction, Data-format, Alignment, Differential-expression, Feature-summarisation, QC
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
EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014

No description available

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014 https://tess.elixir-europe.org/materials/embo-high-throughput-sequencing-data-analysis-cambridge-uk-2014 No description available RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming