Register training material
25 materials found

Authors: Jan Slifka  or Erasmus+ Programme 


Hands-on for 'Refining Genome Annotations with Apollo (eukaryotes)' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, eukaryote, cyoa

Resource type: hands-on tutorial

Hands-on for 'Genomic Data Visualisation with JBrowse' tutorial

The questions this addresses are:
- How can I visualise features or blast data?
- How can I visualise sequencing data in a workflow

The objectives are:
- Build several visualisations in JBrowse
- Have basic familiarity with moving around JBrowse, and loading several data tracks

Keywords: visualisation

Resource type: hands-on tutorial

Hands-on for 'Refining Genome Annotations with Apollo (prokaryotes)' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Masking repeats with RepeatMasker' tutorial

The questions this addresses are:
- How to mask repeats in a genome?
- What is the difference between hard and soft-masking?

The objectives are:
- Use Red and RepeatMasker to soft-mask a newly assembled genome

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Genome assembly using PacBio data' tutorial

The questions this addresses are:
- How to perform a genome assembly with PacBio data ?
- How to check assembly quality ?

The objectives are:
- Assemble a Genome with PacBio data
- Assess assembly quality

Keywords: assembly, assembly, pacbio

Resource type: hands-on tutorial

Hands-on for 'RNA Seq Counts to Viz in R' tutorial

The questions this addresses are:
- How can I create neat visualizations of the data?

The objectives are:
- Describe the role of data, aesthetics, geoms, and layers in ggplot functions.
- Customize plot scales, titles, subtitles, themes, fonts, layout, and orientation.

Scientific topics: Transcriptomics

Keywords: transcriptomics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Introduction to Machine Learning using R' tutorial

The questions this addresses are:
- What are the main categories in Machine Learning algorithms?
- How can I perform exploratory data analysis?
- What are the main part of a clustering process?
- How can a create a decision tree?
- How can I assess a linear regression model?

The...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'CLI Educational Game - Bashcrawl' tutorial

The questions this addresses are:
- How can I move around on my computer?
- How can I see what files and directories I have?
- How can I specify the location of a file or directory on my computer?
- How can I create, copy, and delete files and directories?
- How can I edit files?

The...

Keywords: data-science, game, bash, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Advanced CLI in Galaxy' tutorial

The questions this addresses are:
- How can I combine existing commands to do new things?
- How can I perform the same actions on many different files?
- How can I find files?
- How can I find things in files?

The objectives are:
- Redirect a command's output to a file.
- Process a file...

Keywords: data-science, bash, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Plotting in Python' tutorial

The questions this addresses are:
- How can I create plots using Python in Galaxy?

The objectives are:
- Use the scientific library matplolib to explore tabular datasets

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'CLI basics' tutorial

The questions this addresses are:
- What is a command shell and why would I use one?
- How can I move around on my computer?
- How can I see what files and directories I have?
- How can I specify the location of a file or directory on my computer?
- How can I create, copy, and delete files...

Keywords: data-science, bash, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'SQL Educational Game - Murder Mystery' tutorial

The questions this addresses are:
- Who did the crime?

The objectives are:
- Explore SQL City and discover who committed the murder
- Reinforce your experiences with SQL such as querying, filtering, and joining data.

Keywords: data-science, game, SQL, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Advanced R in Galaxy' tutorial

The questions this addresses are:
- How can I manipulate data using R in Galaxy?
- How do I get started with tabular data from Galaxy in R?

The objectives are:
- Be able to load and explore the shape and contents of a tabular dataset using base R functions.
- Understand factors and how...

Keywords: data-science, R

Resource type: hands-on tutorial

Hands-on for 'dplyr & tidyverse for data processing' tutorial

The questions this addresses are:
- How can I load tabular data into R?
- How can I slice and dice the data to ask questions?

The objectives are:
- Read data with the built-in read.csv
- Read data with dplyr's read_csv
- Use dplyr and tidyverse functions to cleanup data.

Keywords: data-science, R, jupyter-notebook, rmarkdown-notebook

Resource type: hands-on tutorial

Hands-on for 'Introduction to Python' tutorial

The questions this addresses are:
- How can I run Python programs?

The objectives are:
- Learn the fundamentals of programming in Python

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Advanced Python' tutorial

The questions this addresses are:
- How can I analyze data using Python with Numpy and Pandas?

The objectives are:
- Use the scientific libraries pandas and numpy to explore tabular datasets
- Calculate basic statistics about datasets and columns

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'RStudio in Galaxy' tutorial

The questions this addresses are:
- How can I manipulate data using R in Galaxy?

The objectives are:
- Launch RStudio in Galaxy

Keywords: galaxy-interface, interactive-tools

Resource type: hands-on tutorial

Slides for 'Circos' tutorial

The questions this addresses are:
- What is Circos?
- How can I use Circos within Galaxy?
- What are some of the different track types I can plot?

Keywords: visualisation

Resource type: slides

Slides for 'Refining Genome Annotations with Apollo' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, prokaryote

Resource type: slides

Hands-on for 'Quality Control' tutorial

The questions this addresses are:
- How to perform quality control of NGS raw data?
- What are the quality parameters to check for a dataset?
- How to improve the quality of a dataset?

The objectives are:
- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
- Assess long reads...

Keywords: sequence-analysis

Resource type: hands-on tutorial

Slides for 'Mapping' tutorial

The questions this addresses are:
- What is mapping (alignment)?
- What is the BAM format?
- How can we view aligned sequences?

The objectives are:
- Understand the basic concept of mapping
- Learn about factors influencing alignment
- See a genome browser used to better understand your...

Keywords: sequence-analysis

Resource type: slides

Slides for 'Quality Control' tutorial

The questions this addresses are:
- How to control quality of NGS data?
- What are the quality parameters to check for each dataset?
- How to improve the quality of a sequence dataset?

The objectives are:
- Manipulate FASTQ files
- Control quality from a FASTQ file for short and long...

Keywords: sequence-analysis

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