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1561 materials found

PGDH19 - Population Genetics Demographic History: model-based approaches (2019)

Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH19 - Population Genetics Demographic History: model-based approaches (2019) https://tess.elixir-europe.org/materials/pgdh19-population-genetics-demographic-history-model-based-approaches-2019 Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodriguez Vitor Sousa Armando Arredondo Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
PDA19 - Proteomics Data Analysis (2019)

Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis.

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

PDA19 - Proteomics Data Analysis (2019) https://tess.elixir-europe.org/materials/pda19-proteomics-data-analysis-2019 Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis. Lennart Martens Harald Barsnes Lieven Clement Proteomics, Biological databases, Mass spectrometry data Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ELB19F - Entry level Bioinformatics (First course in 2019)

Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis.

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELB19F - Entry level Bioinformatics (First course in 2019) https://tess.elixir-europe.org/materials/elb19f-entry-level-bioinformatics-first-course-in-2019 Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis. David Philip Judge Daniel Sobral Pedro Fernandes Bioinformatics, Sequencing Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ELBS18 - Entry level Bioinformatics (Second course in 2018)

Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELBS18 - Entry level Bioinformatics (Second course in 2018) https://tess.elixir-europe.org/materials/elbs18-entry-level-bioinformatics-second-course-in-2018 Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis David Philip Judge Daniel Sobral Pedro Fernandes Bioinformatics, Sequencing Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018)

Training material for introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq.

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018) https://tess.elixir-europe.org/materials/ader18s-analysis-of-differential-expression-with-rnaseq-second-course-in-2018 Training material for introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq. Daniel Sobral Daniel Faria Daniel Neves RNA-Seq, Genomics, RNA Academia/ Research Institution Industry Non-Profit Organisation Healthcare
CPANG18 - Computational PANGenomics (2018)

Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.

Keywords: Genomics

Resource type: Documentation, Exercise, Handout, Scripts

CPANG18 - Computational PANGenomics (2018) https://tess.elixir-europe.org/materials/cpang18-computational-pangenomics-2018 Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types. Erik Garrison Mikko Rautiainen Jordan Eizenga Genomics Academia/ Research Institution Industry Non-Profit Organisation
PDA18 - Proteomics Data Analysis (2018)

Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis.

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

PDA18 - Proteomics Data Analysis (2018) https://tess.elixir-europe.org/materials/pda18-proteomics-data-analysis-2018 Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis. Lennart Martens Harald Barsnes Lieven Clement Proteomics, Biological databases, Mass spectrometry data Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018)

Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq.

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018) https://tess.elixir-europe.org/materials/ader18f-analysis-of-differential-expression-with-rnaseq-first-course-in-2018 Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq. Daniel Sobral Daniel Faria Daniel Neves RNA-Seq, Genomics, RNA Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ELB18F - Entry level Bioinformatics (First course in 2018)

Training material for entry level course in bioinformatics with a soft introduction to NGS data analysis.

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELB18F - Entry level Bioinformatics (First course in 2018) https://tess.elixir-europe.org/materials/elb18f-entry-level-bioinformatics-first-course-in-2018 Training material for entry level course in bioinformatics with a soft introduction to NGS data analysis. David Philip Judge Daniel Sobral Pedro Fernandes Bioinformatics, Sequencing Academia/ Research Institution Industry Non-Profit Organisation Healthcare
PPB18 - Programming in Python for Biologists (2018)

Training Material that covers the basic concepts of Python, such as calculation, organization of data, reading and writing files, program logic and writing larger programs. All the examples and exercises focus on solving biological problems.

Operations: Data handling, Data retrieval

Keywords: Bioinformatics, Biology, Biological databases

Resource type: Documentation, Exercise, Handout, Scripts

PPB18 - Programming in Python for Biologists (2018) https://tess.elixir-europe.org/materials/ppb18-programming-in-python-for-biologists-2018 Training Material that covers the basic concepts of Python, such as calculation, organization of data, reading and writing files, program logic and writing larger programs. All the examples and exercises focus on solving biological problems. Allegra Via Vincenza Colonna David Philip Judge Bioinformatics, Biology, Biological databases Academia/ Research Institution Industry Non-Profit Organisation Healthcare
3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018)

Training Material focused in 3C-Data Analysis and 3D Chromatin Folding

Keywords: Hi-C

Resource type: Documentation, Exercise, Handout, Scripts

3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018) https://tess.elixir-europe.org/materials/3daroc18-3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding-2018 Training Material focused in 3C-Data Analysis and 3D Chromatin Folding Marc A. Martí-Renom François Serra David Castillo Hi-C Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018)

Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data.

Keywords: Statistics and probability

Resource type: Documentation, Exercise, Handout, Scripts

ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018) https://tess.elixir-europe.org/materials/abstat18-advanced-biostatistics-for-bioinformatics-tool-users-using-r-2018 Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Lisete Sousa Carina Silva Statistics and probability Academia/ Research Institution Industry Non-Profit Organisation Healthcare
PGDH18 - Population Genetics and Demographic History: model-based approaches (2018)

Training material for hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH18 - Population Genetics and Demographic History: model-based approaches (2018) https://tess.elixir-europe.org/materials/pgdh18-population-genetics-and-demographic-history-model-based-approaches-2018 Training material for hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodríguez Armando Arredondo Soto Vitor Sousa Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
PSLS20 - Practical Statistics for the Life Sciences (2020)

Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences.

Keywords: Statistics, General Linear Models

Resource type: Documentation, Exercise, Handout, Scripts

PSLS20 - Practical Statistics for the Life Sciences (2020) https://tess.elixir-europe.org/materials/psls20-practical-statistics-for-the-life-sciences-2020 Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. Lieven Clement Jeroen Gilis Statistics, General Linear Models Academia/ Research Institution Industry Healthcare Non-Profit Organisation
Discussion about unit testing

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Discussion about unit testing https://tess.elixir-europe.org/materials/discussion-about-unit-testing Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
How to use V-pipe (SARS-CoV-2 data)

How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)

Scientific topics: Workflows, Genetic variation, Virology

Operations: Read pre-processing, Alignment, Variant calling

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

How to use V-pipe (SARS-CoV-2 data) https://tess.elixir-europe.org/materials/how-to-use-v-pipe-sars-cov-2-data How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data) Workflows Genetic variation Virology coronavirus, NGS bioinformatics, Variant-calling bioinformaticians Biologists, Genomicists, Computer Scientists
bio.tools documentation

Documentation for the [bio.tools](https://bio.tools) Bioinformatics Tools and Services Discovery Portal.

Scientific topics: Ontology and terminology, Computational biology, Data submission, annotation, and curation, Bioinformatics

Operations: Data retrieval

Keywords: Tools, Curation, Software, Sofware curation, Tool curation

Resource type: Documentation, API reference

bio.tools documentation https://tess.elixir-europe.org/materials/bio-tools-documentation Documentation for the [bio.tools](https://bio.tools) Bioinformatics Tools and Services Discovery Portal. Ontology and terminology Computational biology Data submission, annotation, and curation Bioinformatics Tools, Curation, Software, Sofware curation, Tool curation Researchers Software providers Developers Curators
Integrated DEsign and AnaLysis of small population group trials (IDeAl)

This series of webinars inform stakeholders about the new IDEAL methodology; the main achievements of each WP of the project and the main outcomes of the whole project.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research, Training material

Resource type: Webinar, e-learning

Integrated DEsign and AnaLysis of small population group trials (IDeAl) https://tess.elixir-europe.org/materials/integrated-design-and-analysis-of-small-population-group-trials-ideal This series of webinars inform stakeholders about the new IDEAL methodology; the main achievements of each WP of the project and the main outcomes of the whole project. Rare diseases Rare Diseases & Research, Training material
Bioconductor and R 4.0

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Bioconductor and R 4.0 https://tess.elixir-europe.org/materials/bioconductor-and-r-4-0 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Bioc vs. CRAN build systems

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Bioc vs. CRAN build systems https://tess.elixir-europe.org/materials/bioc-vs-cran-build-systems Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Ås 11 March 2020

Scientific topics: Data management

Operations: Deposition, Data retrieval, Data handling

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop https://tess.elixir-europe.org/materials/slides-from-data-management-planning-workshop-1bb3798d-4e70-423c-87b6-82ac7e5e5c54 Slides from Data Management Planning workshop for Life Science Projects in Ås 11 March 2020 Data management Data management plan, data management PhD students Post Docs Professors
Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Bergen 04 March 2020

Scientific topics: Data management

Operations: Data handling, Data retrieval, Deposition

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop https://tess.elixir-europe.org/materials/slides-from-data-management-planning-workshop Slides from Data Management Planning workshop for Life Science Projects in Bergen 04 March 2020 Data management Data management plan, data management PhD students Post Docs Professors
Rare Disease Pathway and Network Analysis

The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis.

Keywords: Pathway analysis, Biological networks, Network analysis, Pathways

Resource type: Tutorial

Rare Disease Pathway and Network Analysis https://tess.elixir-europe.org/materials/rare-disease-pathway-and-network-analysis The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis. Pathway analysis, Biological networks, Network analysis, Pathways Life Science Researchers
WheatIS DataDiscovery webinar

The [WheatIS project](http://www.wheatis.org/) aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is...

Scientific topics: Data management

Keywords: wheat, information system, data discovery

Resource type: Webinar, Slides, Video

WheatIS DataDiscovery webinar https://tess.elixir-europe.org/materials/wheatis-datadiscovery-webinar The [WheatIS project](http://www.wheatis.org/) aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is endorsed by the [Wheat Initiative](https://www.wheatinitiative.org/). The [WheatIS DataDiscovery tool](https://urgi.versailles.inrae.fr/wheatis/) allows to search data in all the wheat resources around the world. This Webinar described how to use the tool, what data are available, how to join, etc. The replay is available on [Youtube](https://youtu.be/FoVXBhO8arY). Taner Sen Data management wheat, information system, data discovery Researchers Scientists
Data Stewardship Wizard Workshop (Feb 2020)

[Data Stewardship Wizard](ds-wizard.org) brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data management, Data governance

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides

Data Stewardship Wizard Workshop (Feb 2020) https://tess.elixir-europe.org/materials/data-stewardship-wizard-workshop-feb-2020 [Data Stewardship Wizard](ds-wizard.org) brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into per-project questionnaires to be filled by researchers. This workshop explains the core functionality of the Data Stewardship Wizard. Video recording from the workshop is available **[here](https://www.youtube.com/watch?v=aGpr6JFMuiE)**. Data management Data governance Data management plan, data stewardship, FAIR, data management, software tools Researchers data stewards
Update: Bioconductor Images

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Update: Bioconductor Images https://tess.elixir-europe.org/materials/update-bioconductor-images Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Quantifying and lightening the package dependency burden

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Quantifying and lightening the package dependency burden https://tess.elixir-europe.org/materials/quantifying-and-lightening-the-package-dependency-burden Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
How to use Common Workflow Language

**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**

Scientific topics: Workflows

Keywords: commonwl, common workflow language, CWL, Workflows, eLearning, EeLP

Resource type: Installation instructions, Manual

How to use Common Workflow Language https://tess.elixir-europe.org/materials/how-to-use-common-workflow-language **This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).** Rob Finn Michael Crusoe Workflows commonwl, common workflow language, CWL, Workflows, eLearning, EeLP bioinformaticians life scientists programmers
The Turing Way

The Turing Way is a lightly opinionated guide to reproducible data science. Our goal is to provide all the information that researchers need at the start of their projects to ensure that they are easy to reproduce at the end. This also means making sure PhD students, postdocs, PIs, and...

Keywords: Data Science, Reproducibility, Version control, Reproducible Environment, Continuous integration

Resource type: e-learning

The Turing Way https://tess.elixir-europe.org/materials/the-turing-way The Turing Way is a lightly opinionated guide to reproducible data science. Our goal is to provide all the information that researchers need at the start of their projects to ensure that they are easy to reproduce at the end. This also means making sure PhD students, postdocs, PIs, and funding teams know which parts of the “responsibility of reproducibility” they can affect, and what they should do to nudge data science to being more efficient, effective, and understandable. Data Science, Reproducibility, Version control, Reproducible Environment, Continuous integration
Introduction to GitHub

The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub

Keywords: GitHub, Reproducibility

Resource type: Training materials

Introduction to GitHub https://tess.elixir-europe.org/materials/introduction-to-github The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub Gabriella Rustici GitHub, Reproducibility Senior Managers