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799 materials found

BiocCheck-a-thon check in

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

BiocCheck-a-thon check in https://tess.oerc.ox.ac.uk/materials/bioccheck-a-thon-check-in 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.
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.oerc.ox.ac.uk/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.
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.oerc.ox.ac.uk/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.oerc.ox.ac.uk/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.
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.oerc.ox.ac.uk/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 R

Introduction to R

Introduction to R https://tess.oerc.ox.ac.uk/materials/introduction-to-r-5f6e8625-6ab9-452b-9849-0831bcd6cfdb Introduction to R
Initiation GIMP and Inkscape

This course aims at introducing GIMP and Inkscape (free alternatives for Adobe Photoshop and Illustrator) to prepare images for publication, annotate plots and images, and create figures (diagrams, infographics, ...). It is also a prerequisite for the 'Image Ethics and Poster Design' course.

Initiation GIMP and Inkscape https://tess.oerc.ox.ac.uk/materials/initiation-gimp-and-inkscape-f0b0e114-b53e-4857-b921-27c7523c1df9 This course aims at introducing GIMP and Inkscape (free alternatives for Adobe Photoshop and Illustrator) to prepare images for publication, annotate plots and images, and create figures (diagrams, infographics, ...). It is also a prerequisite for the 'Image Ethics and Poster Design' course.
Functional Analysis

Functional characterization of a gene list

Functional Analysis https://tess.oerc.ox.ac.uk/materials/functional-analysis Functional characterization of a gene list
Initiation to Linux Command Line

This training is a prerequisite for all Linux novices who want to follow a training that requires the use of Linux command line (e.g. metagenomics or GATK training).

Initiation to Linux Command Line https://tess.oerc.ox.ac.uk/materials/initiation-to-linux-command-line This training is a prerequisite for all Linux novices who want to follow a training that requires the use of Linux command line (e.g. metagenomics or GATK training).
Metagenomics

Metagenomics

Metagenomics https://tess.oerc.ox.ac.uk/materials/metagenomics-f073df98-ce90-4875-8ece-3769effcf13e Metagenomics
QPCR analysis using qbase+

QPCR analysis using qbase+

QPCR analysis using qbase+ https://tess.oerc.ox.ac.uk/materials/qpcr-analysis-using-qbase QPCR analysis using qbase+
How to write your Data Management Plan

Welcome to this self-study course about research data management. In this course you will learn more about how you can manage your research data. A lot of material of that version of the **Learn to write your DMP** course has been developed by RDM Support of University of Utrecht. With all...

Resource type: Tutorial, e-learning

How to write your Data Management Plan https://tess.oerc.ox.ac.uk/materials/how-to-write-your-data-management-plan Welcome to this self-study course about research data management. In this course you will learn more about how you can manage your research data. A lot of material of that version of the **Learn to write your DMP** course has been developed by RDM Support of University of Utrecht. With all questions about this course you can contact: info.rdm@vib.be. __By VIB Bioinformatics Core, ELIXIR Belgium and Helis Academy__ ![http://www.vib.be/ -20width](https://corefacilities.vib.be/images/logos/bioinformatics_core_rgb_pos.png) * LiaScript: [this course as e-learning resource](https://material.bits.vib.be/courses/?https://raw.githubusercontent.com/vibbits/material-liascript/master/README.md#1) The course consists of 6 chapters, divided in three categories. * Prepare Data collection * Prepare Data documentation - Handle Data storage - Handle Data security - Share Data selection and preservation - Share Data availability for reuse Each chapter starts with an introduction and ends with an assignment to write that part of your data management plan that corresponds with what you have just learned. You are currently in the introd uction chapter. In this chapter you will learn more about the course and the learning environment. The course ends with chapter 7, 'Rounding up'. **Data Management Plans** The assignment throughout the course is to fill your own data management plan. At the end of each chapter you will be asked to log into DMPonline. With the content in this course, you should be able to apply this to your research project. **Questions about the course** If you have technical questions, please contact bits@vib.be. If you have content related questions, please contact RDM Support: info.rdm@vib.be. All feedback is welcome, as this is still a beta version. Based on feedback from users, more content may be added or existing content may be changed to a different form. **Technical requirements** Some activities use HTML5. Make sure your browser has installed the latest updates. If an activity doesn't work, we recommend you use another browser. **Licenses and credits** We wish you a lot of fun with the course and we hope it turns out to be a useful learning experience. The content of the course is adapted from an online course of [University of Utrecht](https://lll-platform-uu.nl/).
Electronic Lab Notebook

This course aims at introducing ELN or E-notebook 2014 by PerkinElmer.

Electronic Lab Notebook https://tess.oerc.ox.ac.uk/materials/electronic-lab-notebook This course aims at introducing ELN or E-notebook 2014 by PerkinElmer.
Basic Bioinformatics Concepts, Databases and Tools

Bioinformatics Introduction

Basic Bioinformatics Concepts, Databases and Tools https://tess.oerc.ox.ac.uk/materials/basic-bioinformatics-concepts-databases-and-tools-a3e816b5-832c-4a1d-8ee8-342c3681157a Bioinformatics Introduction
Protein Structure Analysis

Analyzing the protein structure of your protein-of-interest can be advantageous in multiple ways. It can help you discover regions which are good candidates to interact with other proteins. It can help you discover new domains. It can help with identifying differences with homologuous proteins...

Protein Structure Analysis https://tess.oerc.ox.ac.uk/materials/protein-structure-analysis Analyzing the protein structure of your protein-of-interest can be advantageous in multiple ways. It can help you discover regions which are good candidates to interact with other proteins. It can help you discover new domains. It can help with identifying differences with homologuous proteins and a lot more.
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.oerc.ox.ac.uk/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.
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.oerc.ox.ac.uk/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.
Windows and Rtools 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

Windows and Rtools 4.0 https://tess.oerc.ox.ac.uk/materials/windows-and-rtools-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.
Update from EuroBioc2019 user/developer sessions

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 from EuroBioc2019 user/developer sessions https://tess.oerc.ox.ac.uk/materials/update-from-eurobioc2019-user-developer-sessions 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.
Adding additional compression filters to rhdf5

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

Adding additional compression filters to rhdf5 https://tess.oerc.ox.ac.uk/materials/adding-additional-compression-filters-to-rhdf5 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.
R packages for communicating reproducible research

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...

Keywords: Workshop

R packages for communicating reproducible research https://tess.oerc.ox.ac.uk/materials/r-packages-for-communicating-reproducible-research 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. Workshop
SPARQL



SPARQL https://tess.oerc.ox.ac.uk/materials/sparql 
Cybersecurity Quiz for SIB employees only (internal use)

No description provided.

Cybersecurity Quiz for SIB employees only (internal use) https://tess.oerc.ox.ac.uk/materials/test-sib-security-quiz No description provided.
Bioconductor updates and directions

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 updates and directions https://tess.oerc.ox.ac.uk/materials/bioconductor-updates-and-directions 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 advance science using Bioconductor

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

How to advance science using Bioconductor https://tess.oerc.ox.ac.uk/materials/how-to-advance-science-using-bioconductor 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.
Bioconductor updates

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 updates https://tess.oerc.ox.ac.uk/materials/bioconductor-updates 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.
Improving findability of BioC packages

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

Improving findability of BioC packages https://tess.oerc.ox.ac.uk/materials/improving-findability-of-bioc-packages 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.
BridgeDbR Tutorial

This tutorial describes how to use the BridgeDbR package for identifier mapping.

Keywords: ELIXIR RIR, BridgeDb

BridgeDbR Tutorial https://tess.oerc.ox.ac.uk/materials/bridgedbr-tutorial-865471fb-f50b-40f6-98f0-8096b64751b9 This tutorial describes how to use the BridgeDbR package for identifier mapping. ELIXIR RIR, BridgeDb
Cancer Immuno-Oncology: Bioconductor and beyond

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...

Keywords: Workshop

Cancer Immuno-Oncology: Bioconductor and beyond https://tess.oerc.ox.ac.uk/materials/cancer-immuno-oncology-bioconductor-and-beyond 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. Workshop
Discussion: Guidelines for submitting data to ExperimentHub

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: Guidelines for submitting data to ExperimentHub https://tess.oerc.ox.ac.uk/materials/discussion-guidelines-for-submitting-data-to-experimenthub 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.