Register training material
59 materials found

Difficulty level: Beginner 

and

Resource type: e-learning  or Computer Software  or hands-on tutorial 


Hands-on for 'Identification of the micro-organisms in a beer using Nanopore sequencing' tutorial

The questions this addresses are:
- How can yeast strains in a beer sample be identified?
- How can we process metagenomic data sequenced using Nanopore?

The objectives are:
- Inspect metagenomics data
- Run metagenomics tools
- Identify yeast species contained in a sequenced beer sample...

Scientific topics: Metagenomics

Keywords: metagenomics, nanopore, beer, citizen science, metagenomics

Resource type: hands-on tutorial

Hands-on for 'Upload data to Galaxy' tutorial

The questions this addresses are:
- How to upload data to Galaxy

The objectives are:
- Learn how to upload a file by pasting in a URL
- Learn how to import data from a shared library
- Determine the best strategy to get data into Galaxy

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'Functional annotation of protein sequences' tutorial

The questions this addresses are:
- How to perform functional annotation on protein sequences?

The objectives are:
- Perform functional annotation using EggNOG-mapper and InterProScan

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Prokka' tutorial

The questions this addresses are:
- How can we annotate a bacterial genome?
- How can we visualize annotated genomic features?

The objectives are:
- Load genome into Galaxy
- Annotate genome with Prokka
- View annotations in JBrowse

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 '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?

The objectives are:
- Interact with Galaxy via BioBlend.

Keywords: dev, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Unicycler Assembly' tutorial

The questions this addresses are:
- I have short reads and long reads. How do I assemble a genome?

The objectives are:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with...

Keywords: assembly, prokaryote

Resource type: hands-on tutorial

Hands-on for 'An Introduction to Genome Assembly' tutorial

The questions this addresses are:
- How do we perform a very basic genome assembly from short read data?

The objectives are:
- assemble some paired end reads using Velvet
- examine the output of the assembly.

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'De Bruijn Graph Assembly' tutorial

The questions this addresses are:
- What are the factors that affect genome assembly?
- How does Genome assembly work?

The objectives are:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an assembly...

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with Volcano Plot' tutorial

The questions this addresses are:
- How to generate a volcano plot from RNA-seq data?

The objectives are:
- Create a volcano plot of RNA-seq data to visualize significant genes

Scientific topics: Transcriptomics

Keywords: transcriptomics

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 'Tree thinking for tuberculosis evolution and epidemiology' tutorial

The questions this addresses are:
- What information can I get from a phylogenetic tree?
- How do I estimate a phylogeny?

The objectives are:
- Understand the basic concepts behind phylogenetic trees, as applied to Mycobacterium tuberculosis
- Be able to read and interrogate a phylogeny...

Keywords: evolution, prokaryotes, phylogenetics, evolution, work-in-progress

Resource type: hands-on tutorial

Hands-on for 'Label-free versus Labelled - How to Choose Your Quantitation Method' tutorial

The questions this addresses are:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?

The objectives are:
- Choose your quantitation method.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using SearchGUI and PeptideShaker' tutorial

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

The objectives are:
- Protein identification from LC-MS/MS raw files.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Label-free data analysis using MaxQuant' tutorial

The questions this addresses are:
- How to perform label-free analysis in Maxquant?
- Which are the most abundant proteins in serum?
- How successful was the depletion of those in our experiment?

The objectives are:
- Analysis of human serum proteome samples with label-free quantification...

Scientific topics: Proteomics

Keywords: proteomics, DDA, label-free

Resource type: hands-on tutorial

Hands-on for 'Protein FASTA Database Handling' tutorial

The questions this addresses are:
- How to download protein FASTA databases of a certain organism?
- How to download a contaminant database?
- How to create a decoy database?
- How to combine databases?

The objectives are:
- Creation of a protein FASTA database ready for use with database...

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Metatranscriptomics analysis using microbiome RNA-seq data' tutorial

The questions this addresses are:
- How to analyze metatranscriptomics data?
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?

The objectives are:
- Choose the best approach to analyze metatranscriptomics data
-...

Scientific topics: Metagenomics

Keywords: metagenomics, metatranscriptomics

Resource type: hands-on tutorial

Hands-on for 'Metatranscriptomics analysis using microbiome RNA-seq data (short)' tutorial

The questions this addresses are:
- How to analyze metatranscriptomics data?"
- What information can be extracted of metatranscriptomics data?
- How to assign taxa and function to the identified sequences?

The objectives are:
- Choose the best approach to analyze metatranscriptomics data
...

Scientific topics: Metagenomics

Keywords: metagenomics, metatranscriptomics

Resource type: hands-on tutorial

Hands-on for 'Python - Try & Except' tutorial

The questions this addresses are:
- How do I try to execute code, knowing it might fail?
- What are some situations where this is important?
- How can I write my own exceptions.

The objectives are:
- catch an exception
- raise your own exception

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Files & CSV' tutorial

The questions this addresses are:
- How can I read from a file?
- How can I parse a CSV file?
- How can I write results out

The objectives are:
- Read data from a file
- Write new data to a file
- Use with to ensure the file is closed properly.
- Use the CSV module to parse comma and...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Loops' tutorial

The questions this addresses are:
- How can I make a program do many things?

The objectives are:
- Explain what for loops are normally used for.
- Trace the execution of a simple (unnested) loop and correctly state the values of variables in each iteration.
- Write for loops that use the...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Flow Control' tutorial

The questions this addresses are:
- How can my programs do different things based on data values?

The objectives are:
- Write conditional statements including if, elif, and else branches.
- Correctly evaluate expressions containing and and or.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Basic Types & Type Conversion' tutorial

The questions this addresses are:
- What kinds of data do programs store?
- How can I convert one type to another?

The objectives are:
- Explain key differences between integers and floating point numbers.
- Explain key differences between numbers and character strings.
- Use built-in...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Introductory Graduation' tutorial

The questions this addresses are:
- What all did I learn up until now?

The objectives are:
- Recap all previous modules.
- Use exercises to ensure that all previous knowledge is sufficiently covered.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Functions' tutorial

The questions this addresses are:
- How do I write functions in Python?
- What is a function?
- What do they look like?
- Fill in the missing part of a function

The objectives are:
- Understand the structure of a "function" in order to be able to construct their own functions and predict...

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Python - Math' tutorial

The questions this addresses are:
- How do I do math in Python?

The objectives are:
- Understand the fundamentals of object assignment and math in python and can write simple statements and execute calcualtions in order to be able to summarize the results of calculations and classify valid...

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 'Advanced SQL' tutorial

The questions this addresses are:
- How can I calculate sums, averages, and other summary values?
- How can I combine data from multiple tables?
- How should I format data in a database, and why?
- How can I create, modify, and delete tables and data?
- How can I access databases from...

Keywords: data-science, SQL, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Introduction to SQL' tutorial

The questions this addresses are:
- How can I get data from a database?
- How can I sort a query's results?
- How can I remove duplicate values from a query's results?
- How can I select subsets of data?
- How can I calculate new values on the fly?
- How do databases represent missing...

Keywords: data-science, SQL, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'R basics in Galaxy' tutorial

The questions this addresses are:
- What are the basic features and objects of the R language?

The objectives are:
- Know advantages of analyzing data using R within Galaxy.
- Compose an R script file containing comments, commands, objects, and functions.
- Be able to work with objects...

Keywords: data-science, interactive-tools, R

Resource type: hands-on tutorial