Register training material
20 materials found

Authors: Jan Slifka  or Nicola Soranzo 


Hands-on for 'Calling variants in diploid systems' tutorial

The questions this addresses are:
- How to find variable sites in diploid genomes?

The objectives are:
- Identification of genetic variations using variant calling

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Single-cell quality control with scater' tutorial

The questions this addresses are:
- How to ensure the quality of single-cell RNA-seq data?
- What are the confounding factors that may affect the interpretation of downstream analyses?

The objectives are:
- Examine scRNA-seq data for low-quality cells
- Visualise data with various types of...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell

Resource type: hands-on tutorial

Hands-on for 'Reference-based RNA-Seq data analysis' tutorial

The questions this addresses are:
- What are the steps to process RNA-Seq data?
- How to identify differentially expressed genes across multiple experimental conditions?
- What are the biological functions impacted by the differential expression of genes?

The objectives are:
- Check a...

Scientific topics: Transcriptomics

Keywords: transcriptomics, bulk, rna-seq, collections, drosophila, QC, cyoa

Resource type: hands-on tutorial

Hands-on for 'External Authentication' tutorial

The questions this addresses are:
- How can I connect Galaxy with CAS, SAML, etc.

The objectives are:
- be familiar with configuring Galaxy to use an upstream (proxy) authentication provider
- be able to log in to your Galaxy server with a file-configured user.

Keywords: admin, authentication

Resource type: hands-on tutorial

Hands-on for 'Galaxy Tool Management with Ephemeris' tutorial

The questions this addresses are:
- How to install, update, and maintain Galaxy tools?
- How to extract a list of tools from a workflow or Galaxy instance?

The objectives are:
- Learn about Ephemeris
- Extract a list of tools from a workflow
- Install these tools on a given Galaxy

Keywords: admin, tools, git-gat

Resource type: hands-on tutorial

Hands-on for 'Galaxy 101' tutorial

The questions this addresses are:
- Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22?

The objectives are:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
-...

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'A short introduction to Galaxy' tutorial

The questions this addresses are:
- How to get started in Galaxy

The objectives are:
- Learn how to upload a file
- Learn how to use a tool
- Learn how to view results
- Learn how to view histories
- Learn how to extract and run a workflow

Keywords: introduction, español

Resource type: hands-on tutorial

Hands-on for 'From peaks to genes' tutorial

The questions this addresses are:
- How to use Galaxy?
- How to get from peak regions to a list of gene names?

The objectives are:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
- Learn how histories work
-...

Keywords: introduction

Resource type: hands-on tutorial

Slides for 'Scripting Galaxy using the API and BioBlend' tutorial

The questions this addresses are:
- What is a REST API?
- How to interact with Galaxy programmatically?
- Why and when should I use BioBlend?

Keywords: dev

Resource type: slides

Slides for 'Tool Dependencies and Conda' tutorial

The questions this addresses are:
- How can I connect tools to applications and libraries?
- What are the advantages of declaring dependencies for my tool?
- What are Conda and Bioconda?
- What are Conda recipes and environments?
- How do I find and use existing Conda recipes?
- How do I...

Keywords: dev

Resource type: slides

Slides for 'Tool development and integration into Galaxy' tutorial

The questions this addresses are:
- What is a tool for Galaxy?
- How to write a best-practice tool?
- How to deal with the tool environment?

The objectives are:
- Learn what a tool is and its structure
- Use the Planemo utilities to develop a tool
- Deal with the dependencies
- Write...

Keywords: dev

Resource type: slides

Slides for 'Connecting Galaxy to a compute cluster' tutorial

The questions this addresses are:
- How to connect Galaxy to a compute cluster?
- How can I configure job dependent resources, like cores, memory for my DRM?

The objectives are:
- Understand all components of the Galaxy job running stack
- Understand how the job_conf.xml file controls...

Keywords: admin, features

Resource type: slides

Slides for 'External Authentication' tutorial

The questions this addresses are:
- How can I connect Galaxy with CAS, SAML, etc.

The objectives are:
- be familiar with configuring Galaxy to use an upstream (proxy) authentication provider
- be able to log in to your Galaxy server with a file-configured user.

Keywords: admin

Resource type: slides

Slides for 'Galaxy Tool Management with Ephemeris' tutorial

The questions this addresses are:
- How are tools configured on a Galaxy instance?
- What is the Galaxy Tool Shed?
- How are Galaxy tools installed?
- What is ephemeris and how can it be used to manage tools on a Galaxy instance?

Keywords: admin

Resource type: slides

Slides for 'A Short Introduction to Galaxy' tutorial

The questions this addresses are:
- What is Galaxy?
- Why should I use Galaxy?
- How do I use Galaxy?
- How can I connect with the Galaxy Community?

Keywords: introduction

Resource type: slides

Slides for 'Options for using Galaxy' tutorial

The questions this addresses are:
- Which Galaxy instance should I use?

Keywords: introduction

Resource type: slides

Introduction to 'Introduction to Galaxy Analyses'

Slides for Introduction to Galaxy Analyses

Resource type: slides

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

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

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard 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 governance, Data management

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

Resource type: Video, Webinar, Slides