Register training material
10 materials found

Authors: Jan Slifka  or Alex Ostrovsky 


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

The questions this addresses are:
- How does frequency of mitochondrial polymorphisms change from mother to child?

The objectives are:
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Creating Galaxy tools from Conda Through Deployment' tutorial

The questions this addresses are:
- How do you create a conda package used as a dependency in a Galaxy tool wrapper?
- How do you create a Galaxy tool wrapper and all of its requirements?
- How do you test a Galaxy tool wrapper after it's written?
- How do you deploy a Galaxy tool wrapper?
...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'VGP assembly pipeline' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

The objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality of...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Hands-on for 'VGP assembly pipeline - short version' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

The objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality of...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Hands-on for 'Downstream Single-cell RNA analysis with RaceID' tutorial

The questions this addresses are:
- What is normalisation and why is it necessary?
- How many types of unwanted variation are there?
- How are biological phenotypes clustered?
- What is the difference between PCA and tSNE?
- What is the difference between cell trajectory and cell...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell

Resource type: hands-on tutorial

Slides for 'Plates, Batches, and Barcodes' tutorial

The questions this addresses are:
- What is a batch when it comes to single cells?
- What’s the difference between a barcode and an index?
- What is batch effect and how do you prevent it?
- What is a lane?

The objectives are:
- How to set up plates to prevent batch effect
- Proper...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell

Resource type: slides

Slides for 'Dealing with Cross-Contamination in Fixed Barcode Protocols' tutorial

The questions this addresses are:
- What is cross-contamination?
- What are fixed barcodes?
- Why are plating setups important to know?
- Is it necessary to check barcodes that don't exist in a batch?

The objectives are:
- How to describe a plating setup
- Proper naming conventions when...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell

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