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32 materials found

Keywords: Structures  or BAM 


EMBL-EBI Train Online

If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently.

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems

EMBL-EBI Train Online https://tess.elixir-europe.org/materials/embl-ebi-train-online If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently. Bioinformatics Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems Beginner informatics Life sciences 2018-05-11
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
PDBe: Searching for biological macromolecular structures

PDBe: Searching for biological macromolecular structures from http://www.ebi.ac.uk/training/online/course/pdbe-searching-biological-macromolecular-structure.

Keywords: Proteins, Chemical biology, Structures

PDBe: Searching for biological macromolecular structures https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures PDBe: Searching for biological macromolecular structures from http://www.ebi.ac.uk/training/online/course/pdbe-searching-biological-macromolecular-structure. Proteins, Chemical biology, Structures 2016-05-26
PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure

PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure from http://www.ebi.ac.uk/training/online/course/pdbepisa-identifying-and-interpreting-likely-biolo, added automatically.

Keywords: Proteins, Structures

PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure https://tess.elixir-europe.org/materials/pdbepisa-identifying-and-interpreting-the-likely-biological-assemblies-of-a-protein-structure PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure from http://www.ebi.ac.uk/training/online/course/pdbepisa-identifying-and-interpreting-likely-biolo, added automatically. Proteins, Structures 2016-03-05
PDBeFold: Searching for structural homologues of a protein

PDBeFold: Searching for structural homologues of a protein from http://www.ebi.ac.uk/training/online/course/pdbefold-searching-structural-homologues-protein, added automatically.

Keywords: Proteins, Structures

PDBeFold: Searching for structural homologues of a protein https://tess.elixir-europe.org/materials/pdbefold-searching-for-structural-homologues-of-a-protein PDBeFold: Searching for structural homologues of a protein from http://www.ebi.ac.uk/training/online/course/pdbefold-searching-structural-homologues-protein, added automatically. Proteins, Structures 2016-03-05
PDBeChem: Searching for small molecules and small molecule fragments

PDBeChem: Searching for small molecules and small molecule fragments from http://www.ebi.ac.uk/training/online/course/pdbechem-searching-small-molecules-and-small-molec.

Scientific topics: Small molecules

Keywords: Proteins, Chemical biology, Structures

PDBeChem: Searching for small molecules and small molecule fragments https://tess.elixir-europe.org/materials/pdbechem-searching-for-small-molecules-and-small-molecule-fragments PDBeChem: Searching for small molecules and small molecule fragments from http://www.ebi.ac.uk/training/online/course/pdbechem-searching-small-molecules-and-small-molec. Small molecules Proteins, Chemical biology, Structures 2016-04-22
PDBe: Searching the Protein Data Bank

PDBe: Searching the Protein Data Bank from http://www.ebi.ac.uk/training/online/course/pdbe-searching-protein-data-bank.

Keywords: Proteins, Chemical biology, Structures

PDBe: Searching the Protein Data Bank https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank PDBe: Searching the Protein Data Bank from http://www.ebi.ac.uk/training/online/course/pdbe-searching-protein-data-bank. Proteins, Chemical biology, Structures 2016-05-26
PDBe: Quick tour

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

Keywords: Proteins, Structures

PDBe: Quick tour https://tess.elixir-europe.org/materials/pdbe-quick-tour PDBe: Quick tour from http://www.ebi.ac.uk/training/online/course/pdbe-quick-tour. Proteins, Structures 2016-05-26
PDBe: Exploring a Protein Data Bank (PDB) entry

PDBe: Exploring a Protein Data Bank (PDB) entry from http://www.ebi.ac.uk/training/online/course/pdbe-exploring-protein-data-bank-pdb-entry.

Keywords: Proteins, Chemical biology, Structures

PDBe: Exploring a Protein Data Bank (PDB) entry https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry PDBe: Exploring a Protein Data Bank (PDB) entry from http://www.ebi.ac.uk/training/online/course/pdbe-exploring-protein-data-bank-pdb-entry. Proteins, Chemical biology, Structures 2016-06-14
PDBe: An introduction to search and entry pages: webinar

PDBe: An introduction to search and entry pages: webinar from http://www.ebi.ac.uk/training/online/course/pdbe-introduction-search-and-entry-pages-webinar.

Keywords: Proteins, Chemical biology, Structures

PDBe: An introduction to search and entry pages: webinar https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar PDBe: An introduction to search and entry pages: webinar from http://www.ebi.ac.uk/training/online/course/pdbe-introduction-search-and-entry-pages-webinar. Proteins, Chemical biology, Structures 2016-04-14
Complex Portal: webinar

Complex Portal: webinar from http://www.ebi.ac.uk/training/online/course/complex-portal-webinar.

Keywords: Systems, Ontologies, Proteins, Structures

Complex Portal: webinar https://tess.elixir-europe.org/materials/complex-portal-webinar Complex Portal: webinar from http://www.ebi.ac.uk/training/online/course/complex-portal-webinar. Systems, Ontologies, Proteins, Structures 2016-06-14
Complex Portal: Quick tour

Complex Portal: Quick tour from http://www.ebi.ac.uk/training/online/course/complex-portal-quick-tour.

Keywords: Systems, Ontologies, Proteins, Structures

Complex Portal: Quick tour https://tess.elixir-europe.org/materials/complex-portal-quick-tour Complex Portal: Quick tour from http://www.ebi.ac.uk/training/online/course/complex-portal-quick-tour. Systems, Ontologies, Proteins, Structures 2016-06-14
ChEMBL: Exploring bioactive drug-like molecules

ChEMBL: Exploring bioactive drug-like molecules from http://www.ebi.ac.uk/training/online/course/chembl-exploring-bioactive-drug-molecules.

Keywords: Chemical biology, Structures

ChEMBL: Exploring bioactive drug-like molecules https://tess.elixir-europe.org/materials/chembl-exploring-bioactive-drug-like-molecules ChEMBL: Exploring bioactive drug-like molecules from http://www.ebi.ac.uk/training/online/course/chembl-exploring-bioactive-drug-molecules. Chemical biology, Structures 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
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
Expression estimation

This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed.

Scientific topics: RNA-Seq

Keywords: GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation

Expression estimation https://tess.elixir-europe.org/materials/expression-estimation This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed. RNA-Seq GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation
Mapping Quality Control

Perform QC on aligned data

Keywords: Alignment, BAM, QC

Mapping Quality Control https://tess.elixir-europe.org/materials/mapping-quality-control Perform QC on aligned data Alignment, BAM, QC
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
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 1 - RNA-Seq Analysis

Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer.

Keywords: Alignment, BAM, FASTA, FASTQ, QC

Day 1 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-1-rna-seq-analysis Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer. Alignment, BAM, FASTA, FASTQ, QC
RNA-seq module Frederik Coppens

All material concerning RNA-seq analysis

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, BAM, FASTQ, Feature-summarisation, Pre-processing, QC

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens All material concerning RNA-seq analysis RNA-Seq RNA-Seq, Alignment, BAM, FASTQ, Feature-summarisation, Pre-processing, QC
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
Alignment

Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales.

Scientific topics: RNA-Seq

Keywords: BAM, Populus-tremula, RNA-Seq, QC, Alignment

Alignment https://tess.elixir-europe.org/materials/alignment Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales. RNA-Seq BAM, Populus-tremula, RNA-Seq, QC, Alignment
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