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://www.france-bioinformatique.fr/en/node/1951
http://tess.elixir-uk.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://www.france-bioinformatique.fr/en/node/1957
http://tess.elixir-uk.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://www.france-bioinformatique.fr/en/node/1918
http://tess.elixir-uk.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://www.france-bioinformatique.fr/en/node/1952
http://tess.elixir-uk.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://www.france-bioinformatique.fr/en/node/1958
http://tess.elixir-uk.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://www.france-bioinformatique.fr/en/node/1919
http://tess.elixir-uk.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
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/ChIP-Seq/Bori_Mifsud/README.md
http://tess.elixir-uk.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.
Bori Mifsud
Kathi Zarnack
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/ChIP-Seq/Bori_Mifsud/EMBO_Oct_2014_ChIP_seq_practical_talk.md
http://tess.elixir-uk.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.
Bori Mifsud
Kathi Zarnack
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/ChIP-Seq/Bori_Mifsud/EMBO_Oct_2014_ChIP_seq_practical.md
http://tess.elixir-uk.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.
Bori Mifsud
Kathi Zarnack
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/Variant-calling/README.md
http://tess.elixir-uk.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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Jenny_Drnevich/Day4.md
http://tess.elixir-uk.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.
Jenny Drnevich @jenny
Radhika Khetani @radhika
Jessica Kirkpatrick krkptrc2@illinois.edu
Exploratory-analysis, Differential-expression, Statistical-model, Annotation
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/README.md
http://tess.elixir-uk.org/materials/nicolas-delhomme-and-bastian-schiffthaler
This merely lists the various courses at which we taught RNA-Seq data
@delhomme
@bastian
RNA-Seq
FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/ChIP-Seq/README.md
http://tess.elixir-uk.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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014/00_EMBO-October-2014-Tutorial.md
http://tess.elixir-uk.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.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Jenny_Drnevich/README.md
http://tess.elixir-uk.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
Jenny Drnevich @jenny
Radhika Khetani @radhika
Jessica Kirkpatrick krkptrc2@illinois.edu
RNA-Seq
RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md
http://tess.elixir-uk.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.
Nicolas Delhomme @delhomme
Robinson K.
Mähler N.
Bastian Schiffthaler @bastian
Oenskog J.
Albrectsen B.
Ingvarsson P. K.
Hvidsten T. R.
Jansson S.
Street N. R.
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014.md
http://tess.elixir-uk.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.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
RNA-Seq
FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/ChIP-Seq/Anna_Poetsch/README.md
http://tess.elixir-uk.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.
Anna Poetsch
based partially on material from Bori Mifsud and Ernest Turro
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Nicolas_Delhomme/EMBO-Oct-2014/04_EMBO-October-2014-Annotation.md
http://tess.elixir-uk.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.
Nicolas Delhomme @delhomme
Bastian Schiffthaler @bastian
RNA-Seq
GFF3, Populus-tremula, RNA-Seq, Annotation
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Courses/201411-EMBO-High-Throughput-Sequencing-Data-Analysis.md
http://tess.elixir-uk.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