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30 materials found

Keywords: Exploratory-analysis  or Annotation 


Exploring Microscope Platform

How to use the Microscope Platform to annotate and analyze microbial genomes.

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics

Exploring Microscope Platform https://tess.elixir-europe.org/materials/exploring-microscope-platform How to use the Microscope Platform to annotate and analyze microbial genomes. Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics
REPET: TEdenovo tutorial

The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE

Keywords: Annotation, Genomics

REPET: TEdenovo tutorial https://tess.elixir-europe.org/materials/repet-tedenovo-tutorial The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE Annotation, Genomics
Chip Seq: Annotation and visualization Lesson

How to add biological meaning to peaks

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Lesson https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-lesson How to add biological meaning to peaks Annotation, Chip-seq, Data Visualization, NGS
Exploring microbiomes with the MicroScope Platform

This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational...

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics

Exploring microbiomes with the MicroScope Platform https://tess.elixir-europe.org/materials/exploring-microbiomes-with-the-microscope-platform This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational annotation of bacterial genomes: synteny Automatic functional assignation and expert annotation of genes Relational annotation of bacterial genomes: phylogenetic profiles Relational annotation of bacterial genomes: pan-genome analysis Relational annotation of bacterial genomes: metabolic pathways Syntactic re-annotation of public microbial genomes Syntactic annotation of microbial genomes Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics
REPET: TEdannot Tutorial

TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo

Keywords: Annotation, Genomics

REPET: TEdannot Tutorial https://tess.elixir-europe.org/materials/repet-tedannot-tutorial TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo Annotation, Genomics
Chip Seq: Annotation and visualization Tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Tutorial https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Annotation, Chip-seq, Data Visualization, NGS
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
ChIP-seq analysis using R

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a...

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming

ChIP-seq analysis using R https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-5049bc9c-9bbb-4a6b-9244-37ed3980da0e ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a theoretical background and the means to perform peak calling and differential binding analysis. ChIP-Seq, Experimental-design, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming
ChIP-seq analysis using R - Practical talk

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This practical is an introduction to ChIP-seq data analysis mainly using R, some command line based peak-callers and online software. It provides means to...

Keywords: ChIP-Seq, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming

ChIP-seq analysis using R - Practical talk https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-practical-talk ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This practical is an introduction to ChIP-seq data analysis mainly using R, some command line based peak-callers and online software. It provides means to perform peak calling, annotation, motif search and differential binding analysis. ChIP-Seq, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming
ChIP-seq analysis using R - Practical

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This practical is an introduction to ChIP-seq data analysis mainly using R, some command line based peak-callers and online software. It provides means to...

Keywords: ChIP-Seq, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming

ChIP-seq analysis using R - Practical https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-practical ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This practical is an introduction to ChIP-seq data analysis mainly using R, some command line based peak-callers and online software. It provides means to perform peak calling, annotation, motif search and differential binding analysis. ChIP-Seq, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming
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
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
ChIP-Seq

No description available

Keywords: ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation

ChIP-Seq https://tess.elixir-europe.org/materials/chip-seq No description available ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation
Tutorial

This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.

Scientific topics: RNA-Seq

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

Tutorial https://tess.elixir-europe.org/materials/tutorial This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming
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
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
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
ChIP-seq analysis using R

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a...

Keywords: ChIP-Seq, Experimental-design, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation

ChIP-seq analysis using R https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a theoretical background and the means to perform peak calling and differential binding analysis. ChIP-Seq, Experimental-design, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation
Annotation

This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses.

Scientific topics: RNA-Seq

Keywords: GFF3, Populus-tremula, RNA-Seq, Annotation

Annotation https://tess.elixir-europe.org/materials/annotation This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses. RNA-Seq GFF3, Populus-tremula, RNA-Seq, Annotation
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
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