Search Tutorials

Basics of machine learning

Statistics and machine learning

Anup Kumar

Age prediction using machine learning

Statistics and machine learning

Ekaterina Polkh, Anup Kumar

Classification in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

Machine learning: classification and regression

Statistics and machine learning

Anup Kumar, Bérénice Batut

Regression in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

Introduction to Machine Learning using R

Statistics and machine learning

interactive-tools

Fotis E. Psomopoulos, Erasmus+ Programme

Machine Learning Modeling of Anticancer Peptides

Proteomics

ML cancer

Jayadev Joshi, Daniel Blankenberg

PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis

Statistics and machine learning

Machine learning Pan-cancer cancer biomarkers oncogenes and tumor suppressor genes

Vijay, Daniel Blankenberg

Clustering in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar

A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy

Statistics and machine learning

interactive-tools machine-learning deep-learning jupyter-lab image-segmentation protein-3D-structure

Anup Kumar

Running Ansible on your remote machine

FAQ

Helena Rasche

Deep Learning (Part 3) - Convolutional neural networks (CNN)

Statistics and machine learning

Kaivan Kamali

Deep Learning (Part 2) - Recurrent neural networks (RNN)

Statistics and machine learning

Kaivan Kamali

Reference Data with CVMFS without Ansible

Galaxy Server administration

Simon Gladman, Helena Rasche

Introduction to deep learning

Statistics and machine learning

Anup Kumar, Alireza Khanteymoori

Visualize EBV cube data with Panoply netCDF viewer

Ecology

interactive-tools EBV cube Data visualization

Yvan Le Bras, Coline Royaux, Marie Josse, Anne Fouilloux

Visualize Climate data with Panoply netCDF viewer

Climate

interactive-tools

Anne Fouilloux

Running Jobs on Remote Resources with Pulsar

Galaxy Server administration

ansible jobs git-gat

Nate Coraor, Simon Gladman, Marius van den Beek, Helena Rasche, Gianmauro Cuccuru

Ansible

Galaxy Server administration

ansible

Helena Rasche, Saskia Hiltemann

Galaxy 101

Introduction to Galaxy Analyses

Saskia Hiltemann, Nicola Soranzo, Clemens Blank, Anton Nekrutenko, Björn Grüning, Anne Pajon, Helena Rasche

How to reproduce published Galaxy analyses

Introduction to Galaxy Analyses

Melanie Föll, Anne Fouilloux

Deep Learning (Part 1) - Feedforward neural networks (FNN)

Statistics and machine learning

Kaivan Kamali

Image classification in Galaxy with fruit 360 dataset

Statistics and machine learning

Kaivan Kamali

Evaluating and ranking a set of pathways based on multiple metrics

Synthetic Biology

Kenza Bazi-Kabbaj, Thomas Duigou, Joan Hérisson, Guillaume Gricourt, Ioana Popescu, Jean-Loup Faulon

MaxQuant and MSstats for the analysis of TMT data

Proteomics

DDA TMT

Klemens Fröhlich, Melanie Föll, Matthias Fahrner

Text-mining with the SimText toolset

Statistics and machine learning

interactive-tools

Marie Gramm, Dennis Lal group, Daniel Blankenberg

Deploying Tailscale/Headscale for private mesh networking

Galaxy Server administration

wireguard networking

Deploying a compute cluster in OpenStack via Terraform

Galaxy Server administration

terraform deploying cloud

Helena Rasche

Small Non-coding RNA Clustering using BlockClust

Transcriptomics

Pavankumar Videm

Deploying Wireguard for private mesh networking

Galaxy Server administration

wireguard networking

Label-free versus Labelled - How to Choose Your Quantitation Method

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Chloroplast genome assembly

Assembly

plants nanopore

Anna Syme

Galaxy Tool Management with Ephemeris

Galaxy Server administration

tools git-gat

Martin Čech, Helena Rasche, Nicola Soranzo

How can I create a tutorial skeleton from a Galaxy workflow?

FAQ

Saskia Hiltemann

Galaxy Monitoring with Telegraf and Grafana

Galaxy Server administration

ansible monitoring git-gat

Helena Rasche

RAD-Seq de-novo data analysis

Ecology

RAD-seq Genetic composition EBV class Species populations EBV class EBV dataset EBV workflow

Yvan Le Bras

Galaxy Interactive Tools

Development in Galaxy

Estelle Ancelet, Yvan Le Bras, Cameron Hyde, Lain Pavot, Anthony Bretaudeau, Helena Rasche

Mapping

Sequence analysis

Joachim Wolff, Bérénice Batut, Helena Rasche

Pre-processing of 10X Single-Cell RNA Datasets

Transcriptomics

single-cell 10x

Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg, Wendi Bacon

RAD-Seq Reference-based data analysis

Ecology

RAD-seq Genetic composition EBV class Species population EBV class EBV dataset EBV workflow

Yvan Le Bras

Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab

Climate

interactive-tools

Anne Fouilloux

Peptide and Protein ID using SearchGUI and PeptideShaker

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Enable upload via FTP

Galaxy Server administration

data git-gat

Lucille Delisle

Galaxy Installation with Ansible

Galaxy Server administration

ansible deploying git-gat

Peptide and Protein ID using OpenMS tools

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Managing Galaxy on Kubernetes

Galaxy Server administration

kubernetes

Nuwan Goonasekera, Enis Afgan, Alex Mahmoud, Pablo Moreno, John Davis

How to read a Diff

FAQ

Helena Rasche

Multisample Analysis

Using Galaxy and Managing your Data

collections

Anton Nekrutenko, Anne Pajon

How I learned to stop worrying and love the systemd

Galaxy Server administration

ansible systemd

CLIP-Seq data analysis from pre-processing to motif detection

Transcriptomics

Florian Heyl, Daniel Maticzka, Bérénice Batut

Reference Data with CVMFS

Galaxy Server administration

ansible git-gat

Simon Gladman, Helena Rasche

Data Libraries

Galaxy Server administration

ansible storage git-gat

Helena Rasche, Saskia Hiltemann

Single-cell quality control with scater

Transcriptomics

single-cell

Graham Etherington, Nicola Soranzo

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Climate

pangeo

Anne Fouilloux

Automation with Jenkins

Galaxy Server administration

ansible automation

Helena Rasche

From small to large-scale genome comparison

Genome Annotation

Esteban Perez-Wohlfeil

High Throughput Molecular Dynamics and Analysis

Computational chemistry

Simon Bray, Tharindu Senapathi, Christopher Barnett, Björn Grüning

JavaScript plugins

Development in Galaxy

Saskia Hiltemann, Youri Hoogstrate, Björn Grüning, Aysam Guerler, Dannon Baker

Getting your hands-on climate data

Climate

Anne Fouilloux

Unicycler Assembly

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Simon Gladman

Pangeo Notebook in Galaxy - Introduction to Xarray

Climate

pangeo interactive-tools jupyter-notebook jupyter-notebook

Anne Fouilloux

Visualization of Climate Data using NetCDF xarray Map Plotting

Ecology

pangeo

Soumya Jha

Upgrading Galaxy

Galaxy Server administration

ansible

Simon Gladman

InterMine integration with Galaxy

Using Galaxy and Managing your Data

Daniela Butano, Yo Yehudi

Identification of the micro-organisms in a beer using Nanopore sequencing

Metagenomics

nanopore beer citizen science metagenomics

Refining Genome Annotations with Apollo (eukaryotes)

Genome Annotation

eukaryote cyoa

Anthony Bretaudeau, Erasmus+ Programme

Additional resources to learn more about proteomic data analysis

FAQ

Melanie Föll

metaQuantome 3: Taxonomy

Proteomics

microbiome

Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar

Reference-based RNAseq data analysis (long)

Transcriptomics

work-in-progress

Anton Nekrutenko

Refining Genome Annotations with Apollo (prokaryotes)

Genome Annotation

prokaryote

Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus+ Programme

ToolFactory: Generating Tools From Simple Scripts

Development in Galaxy

Ross Lazarus, Helena Rasche

Regional GAM

Ecology

Species populations EBV class Species traits EBV class EBV dataset EBV workflow

Clara Urfer, Elisa Michon, Yvan Le Bras, Bérénice Batut, Simon Benateau

Writing Automated Tests for Galaxy

Development in Galaxy

John Davis, John Chilton

Galaxy Database schema

Galaxy Server administration

Hans-Rudolf Hotz, Björn Grüning

Compute and analyze biodiversity metrics with PAMPA toolsuite

Ecology

Species population EBV class Community composition EBV class EBV dataset EBV workflow modeling

Coline Royaux, Yvan Le Bras, Jean-Baptiste Mihoub

From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis

Variant Analysis

covid19

Marius van den Beek, Dave Clements, Daniel Blankenberg, Anton Nekrutenko

Peptide Library Data Analysis

Proteomics

Jayadev Joshi, Daniel Blankenberg

NGS data logistics

Introduction to Galaxy Analyses

Anton Nekrutenko, Marius van den Beek, Dave Clements, Daniel Blankenberg

MaxQuant and MSstats for the analysis of label-free data

Proteomics

label-free

Melanie Föll, Matthias Fahrner

Galaxy 101 for everyone

Introduction to Galaxy Analyses

Anne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann

Using dataset collections

Using Galaxy and Managing your Data

collections

Anton Nekrutenko

Genome annotation with Funannotate

Genome Annotation

eukaryote

Mass spectrometry imaging: Loading and exploring MSI data

Proteomics

mouse imaging

Melanie Föll, Björn Grüning

Masking repeats with RepeatMasker

Genome Annotation

eukaryote

Anthony Bretaudeau, Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Erasmus+ Programme, Jonathan Kreplak

From peaks to genes

Introduction to Galaxy Analyses

Anne Pajon, Clemens Blank, Bérénice Batut, Björn Grüning, Nicola Soranzo, Dilmurat Yusuf, Sarah Peter, Helena Rasche

Performant Uploads with TUS

Galaxy Server administration

Marius van den Beek, Helena Rasche, Lucille Delisle

The workflows contain several Query tabular for text manipulation, is there a tutorial for that?

FAQ

Subina Mehta

Use Singularity containers for running Galaxy jobs

Galaxy Server administration

jobs ansible git-gat

Torfinn Nome, Marius van den Beek, Matthias Bernt, Helena Rasche

Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring

Computational chemistry

covid19

Simon Bray

ToolFactory: Generating Tools From More Complex Scripts

Development in Galaxy

Ross Lazarus

Making sense of a newly assembled genome

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Helena Rasche

Setting up molecular systems

Computational chemistry

Christopher Barnett, Simon Bray, Nadia Goué

Contributing to BioBlend as a developer

Development in Galaxy

Erik Schill, Simon Bray

Identifying tuberculosis transmission links: from SNPs to transmission clusters

Evolution

work-in-progress

Galo A. Goig, Daniela Brites, Christoph Stritt

Submitting sequence data to ENA

Using Galaxy and Managing your Data

covid19

Miguel Roncoroni, Bert Droesbeke

A short introduction to Galaxy

Introduction to Galaxy Analyses

español

Anna Syme, Nicola Soranzo

Group tags for complex experimental designs

Using Galaxy and Managing your Data

Marius van den Beek

Cleaning GBIF data for the use in Ecology

Ecology

gbif data management data cleaning

Yvan Le Bras, Simon Benateau

metaQuantome 2: Function

Proteomics

microbiome

Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar

Galaxy Monitoring with gxadmin

Galaxy Server administration

monitoring ansible git-gat

Helena Rasche

Upload data to Galaxy

Introduction to Galaxy Analyses

work-in-progress

Bérénice Batut

Trajectory Analysis using Monocle3

Transcriptomics

single-cell trajectory-analysis paper-replication

Contributing a New Feature to Galaxy Core

Development in Galaxy

John Chilton, John Davis

Galaxy Webhooks

Development in Galaxy

Clemens Blank, Martin Čech, Björn Grüning

JupyterLab in Galaxy

Using Galaxy and Managing your Data

interactive-tools

Name tags for following complex histories

Using Galaxy and Managing your Data

Helena Rasche

Nucleoli segmentation and feature extraction using CellProfiler

Imaging

Beatriz Serrano-Solano, Jean-Karim Hériché

Rule Based Uploader

Using Galaxy and Managing your Data

collections tags

John Chilton, Helena Rasche

Genome assembly using PacBio data

Assembly

assembly pacbio

Anthony Bretaudeau, Alexandre Cormier, Erwan Corre, Laura Leroi, Stéphanie Robin, Erasmus+ Programme

Introduction to image analysis using Galaxy

Imaging

Thomas Wollmann, Saskia Hiltemann

Network analysis with Heinz

Transcriptomics

metatranscriptomics network analysis

Chao (Cico) Zhang

De novo transcriptome assembly, annotation, and differential expression analysis

Transcriptomics

work-in-progress

Anthony Bretaudeau, Gildas Le Corguillé, Erwan Corre, Xi Liu

Rule Based Uploader: Advanced

Using Galaxy and Managing your Data

collections tags

John Chilton, Helena Rasche

Analyses of metagenomics data - The global picture

Metagenomics

Saskia Hiltemann, Bérénice Batut

Protein FASTA Database Handling

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

EncyclopeDIA

Proteomics

DIA

Emma Leith, Subina Mehta, James Johnson, Pratik Jagtap, Timothy J. Griffin

Removal of human reads from SARS-CoV-2 sequencing data

Sequence analysis

covid19

Wolfgang Maier

De Bruijn Graph Assembly

Assembly

Simon Gladman, Helena Rasche, Saskia Hiltemann

Extracting Workflows from Histories

Using Galaxy and Managing your Data

workflows

Dave Clements

Automating Galaxy workflows using the command line

Using Galaxy and Managing your Data

workflows variant-analysis covid19

Simon Bray, Wolfgang Maier

Using Workflow Parameters

Using Galaxy and Managing your Data

workflows

Marius van den Beek, Helena Rasche

Proteogenomics 3: Novel peptide analysis

Proteomics

proteogenomics

Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar

RNA Seq Counts to Viz in R

Transcriptomics

interactive-tools

Bérénice Batut, Fotis E. Psomopoulos, Toby Hodges, Erasmus+ Programme

Genomic Data Visualisation with JBrowse

Visualisation

Helena Rasche, Saskia Hiltemann, Erasmus+ Programme

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Proteomics

DDA SILAC

Florian Christoph Sigloch, Björn Grüning, Matthias Fahrner

Creating Galaxy tools from Conda Through Deployment

Development in Galaxy

Alex Ostrovsky, Dave B., Matthias Bernt

Formation of the Super-Structures on the Inactive X

Epigenetics

ChIP-seq

Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani

Analysis of molecular dynamics simulations

Computational chemistry

Christopher Barnett, Tharindu Senapathi, Simon Bray, Nadia Goué

DIA Analysis using OpenSwathWorkflow

Proteomics

DIA

Matthias Fahrner, Melanie Föll

Inferring Trajectories using Python (Jupyter Notebook) in Galaxy

Transcriptomics

single-cell 10x paper-replication interactive-tools

Use Jupyter notebooks in Galaxy

Using Galaxy and Managing your Data

Delphine Lariviere

Visualization of RNA-Seq results with Volcano Plot in R

Transcriptomics

interactive-tools

Maria Doyle

RStudio in Galaxy

Using Galaxy and Managing your Data

interactive-tools

Bérénice Batut, Fotis E. Psomopoulos, Toby Hodges, Erasmus+ Programme

Metabarcoding/eDNA through Obitools

Ecology

Genetic composition EBV class Community composition EBV class EBV dataset EBV workflow eDNA Metabarcoding

Coline Royaux, Olivier Norvez, Eric Coissac, Frédéric Boyer, Yvan Le Bras

Pre-processing of Single-Cell RNA Data

Transcriptomics

single-cell

Mehmet Tekman, Bérénice Batut, Anika Erxleben, Wolfgang Maier

Mass spectrometry : GC-MS analysis with metaMS package

Metabolomics

work-in-progress

Julien Saint-Vanne

16S Microbial analysis with Nanopore data

Metagenomics

nanopore

Cristóbal Gallardo

GO Enrichment Analysis

Transcriptomics

IGC Bioinformatics Unit, Maria Doyle

metaQuantome 1: Data creation

Proteomics

microbiome

Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane

Running molecular dynamics simulations using NAMD

Computational chemistry

work-in-progress

Christopher Barnett, Tharindu Senapathi, Simon Bray

RNA-RNA interactome data analysis

Transcriptomics

Pavankumar Videm

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Epigenetics

Joachim Wolff, Fidel Ramirez, Vivek Bhardwaj, Ekaterina Polkh

Running molecular dynamics simulations using GROMACS

Computational chemistry

Simon Bray

Metaproteomics tutorial

Proteomics

microbiome

Timothy J. Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta

DNA Methylation data analysis

Epigenetics

Joachim Wolff, Devon Ryan

Introduction to Genomics and Galaxy

Introduction to Galaxy Analyses

Dave Clements, Cristóbal Gallardo

Data Manipulation Olympics

Introduction to Galaxy Analyses

cyoa

VGP assembly pipeline

Assembly

pacbio eukaryote VGP

Delphine Lariviere, Alex Ostrovsky, Cristóbal Gallardo, Anna Syme, Linelle Abueg, Brandon Pickett, Giulio Formenti, Marcella Sozzoni

VGP assembly pipeline - short version

Assembly

pacbio eukaryote VGP

Delphine Lariviere, Alex Ostrovsky, Cristóbal Gallardo, Brandon Pickett, Linelle Abueg

Label-free data analysis using MaxQuant

Proteomics

DDA label-free

Melanie Föll, Matthias Fahrner

Reference-based RNA-Seq data analysis

Transcriptomics

bulk rna-seq collections drosophila QC cyoa

Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle

Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

Assembly

covid19

Wolfgang Maier

Visualisation with Circos

Visualisation

Saskia Hiltemann, Helena Rasche, Cristóbal Gallardo

SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis

Using Galaxy and Managing your Data

ncbi covid19

Jon Trow, Adelaide Rhodes

RNA-Seq analysis with AskOmics Interactive Tool

Transcriptomics

Xavier Garnier, Anthony Bretaudeau, Anne Siegel, Olivier Dameron, Mateo Boudet

Infinium Human Methylation BeadChip

Epigenetics

Katarzyna Murat, Krzysztof Poterlowicz

Calling variants in non-diploid systems

Variant Analysis

prokaryote

Anton Nekrutenko, Alex Ostrovsky

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Variant Analysis

cancer cyoa

Jasper Ouwerkerk, Wolfgang Maier, Helena Rasche, Saskia Hiltemann

ATAC-Seq data analysis

Epigenetics

Lucille Delisle, Maria Doyle, Florian Heyl

Tree thinking for tuberculosis evolution and epidemiology

Evolution

prokaryotes phylogenetics evolution work-in-progress

Christoph Stritt, Daniela Brites, Galo A. Goig

Generating a single cell matrix using Alevin

Transcriptomics

single-cell 10x paper-replication español

Calling variants in diploid systems

Variant Analysis

Anton Nekrutenko, Nicola Soranzo

CRISPR screen analysis

Genome Annotation

genome editing CRISPR essential genes cell line

Maria Doyle, Kenji Fujihara, Twishi Gulati

1: RNA-Seq reads to counts

Transcriptomics

collections mouse QC

Maria Doyle, Belinda Phipson, Harriet Dashnow

Downstream Single-cell RNA analysis with RaceID

Transcriptomics

single-cell

Mehmet Tekman, Alex Ostrovsky

Essential genes detection with Transposon insertion sequencing

Genome Annotation

bacteria tnseq essential genes

Delphine Lariviere, Bérénice Batut

Clustering 3K PBMCs with Scanpy

Transcriptomics

single-cell 10x

Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman

Comparative gene analysis in unannotated genomes

Genome Annotation

evolution annotation vgp cookbook eukaryote prokaryote

Anton Nekrutenko

Mass spectrometry: LC-MS analysis

Metabolomics

Mélanie Petera, Gildas Le Corguillé, Jean-François Martin, Yann Guitton, Workflow4Metabolomics core team

Mass spectrometry: LC-MS data processing

Metabolomics

Mélanie Petera, Workflow4Metabolomics core team

Filter, Plot and Explore Single-cell RNA-seq Data

Transcriptomics

single-cell 10x paper-replication español interactive-tools

Galaxy Interactive Tools

Galaxy Server administration

ansible interactive-tools

Nate Coraor, Simon Gladman, Helena Rasche, Anthony Bretaudeau

Mass spectrometry: LC-MS preprocessing with XCMS

Metabolomics

Mélanie Petera, Jean-François Martin, Gildas Le Corguillé, Workflow4Metabolomics core team

Generic plugins

Development in Galaxy

Saskia Hiltemann, Youri Hoogstrate

Genome Assembly of MRSA using Illumina MiSeq Data

Assembly

illumina assembly amr

Mass spectrometry imaging: Examining the spatial distribution of analytes

Metabolomics

Melanie Föll, Maren Stillger

Biomarker candidate identification

Proteomics

DDA human

Florence Combes, David Christiany, Valentin Loux, Yves Vandenbrouck

Exome sequencing data analysis for diagnosing a genetic disease

Variant Analysis

Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning

Antibiotic resistance detection

Metagenomics

nanopore plasmids assembly amr

Willem de Koning, Saskia Hiltemann

Mass spectrometry imaging: Finding differential analytes

Metabolomics

Melanie Föll

Calling very rare variants

Variant Analysis

work-in-progress

Anton Nekrutenko, Nick Stoler

Library Generation for DIA Analysis

Proteomics

DIA

Matthias Fahrner, Melanie Föll

Whole transcriptome analysis of Arabidopsis thaliana

Transcriptomics

miRNA plants

Cristóbal Gallardo, Pavankumar Videm, Beatriz Serrano-Solano

2: RNA-seq counts to genes

Transcriptomics

limma-voom mouse QC

Maria Doyle, Belinda Phipson, Jovana Maksimovic, Anna Trigos, Matt Ritchie, Harriet Dashnow, Shian Su, Charity Law

Identification of somatic and germline variants from tumor and normal sample pairs

Variant Analysis

Wolfgang Maier

M. tuberculosis Variant Analysis

Variant Analysis

prokaryote

Peter van Heusden, Simon Gladman, Thoba Lose

An Introduction to Genome Assembly

Assembly

Simon Gladman

Understanding Barcodes

Transcriptomics

single-cell

Mehmet Tekman

Analyse HeLa fluorescence siRNA screen

Imaging

Thomas Wollmann

Somatic Variant Discovery from WES Data Using Control-FREEC

Variant Analysis

Khaled Jum'ah, Katarzyna Murat, Wolfgang Maier, David Salgado, Krzysztof Poterlowicz

Analysis of plant scRNA-Seq Data with Scanpy

Transcriptomics

single-cell plants paper-replication

Mehmet Tekman, Beatriz Serrano-Solano, Cristóbal Gallardo, Pavankumar Videm

Combining datasets after pre-processing

Transcriptomics

single-cell 10x paper-replication español

Object tracking using CellProfiler

Imaging

Yi Sun, Beatriz Serrano-Solano, Jean-Karim Hériché

Long non-coding RNAs (lncRNAs) annotation with FEELnc

Genome Annotation

eukaryote

Quality Control

Sequence analysis

Bérénice Batut, Maria Doyle, Alexandre Cormier, Anthony Bretaudeau, Laura Leroi, Erwan Corre, Stéphanie Robin, Erasmus+ Programme

Understanding Galaxy history system

Using Galaxy and Managing your Data

Anton Nekrutenko, Martin Čech, Helena Rasche

Genome Assembly of MRSA using Oxford Nanopore MinION Data

Assembly

nanopore assembly amr

De novo transcriptome reconstruction with RNA-Seq

Transcriptomics

Mallory Freeberg, Mo Heydarian

3: RNA-seq genes to pathways

Transcriptomics

mouse

Maria Doyle, Belinda Phipson

Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

Variant Analysis

covid19

Wolfgang Maier, Bérénice Batut

Preparing genomic data for phylogeny reconstruction

Ecology

phylogeny data handling functional annotation

Miguel Roncoroni, Brigida Gallone

IGV Introduction

Introduction to Galaxy Analyses

Anton Nekrutenko, Joachim Wolff, Anne Pajon

Species distribution modeling

Ecology

interactive-tools modeling gbif species populations EBV class

Elisa Michon, Yvan Le Bras, Bérénice Batut

Creating, Editing and Importing Galaxy Workflows

Using Galaxy and Managing your Data

workflows

Marius van den Beek

Mapping and molecular identification of phenotype-causing mutations

Variant Analysis

Wolfgang Maier

Connecting Galaxy to a compute cluster

Galaxy Server administration

jobs ansible git-gat

Nate Coraor, Björn Grüning, Helena Rasche

Detection and quantitation of N-termini (degradomics) via N-TAILS

Proteomics

Florian Christoph Sigloch, Björn Grüning

Proteogenomics 2: Database Search

Proteomics

proteogenomics

Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Climate

interactive-tools

Anne Fouilloux, Hui Tang

Genome Assembly Quality Control

Assembly

assembly quality control

Anthony Bretaudeau, Alexandre Cormier, Erwan Corre, Laura Leroi, Stéphanie Robin

Interval-Wise Testing for omics data

Statistics and machine learning

Marzia A Cremona, Fabio Cumbo

Identification of the binding sites of the Estrogen receptor

Epigenetics

ChIP-seq work-in-progress

Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez

Protein-ligand docking

Computational chemistry

Simon Bray

Galaxy Installation on Kubernetes

Galaxy Server administration

kubernetes

Pablo Moreno, Enis Afgan, Nuwan Goonasekera, Alex Mahmoud, John Davis

Visualization of RNA-Seq results with CummeRbund

Transcriptomics

Andrea Bagnacani

Protein target prediction of a bioactive ligand with Align-it and ePharmaLib

Computational chemistry

Aurélien F. A. Moumbock, Simon Bray

Proteogenomics 1: Database Creation

Proteomics

proteogenomics

Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar

Bulk RNA Deconvolution with MuSiC

Transcriptomics

single-cell mouse human deconvolution bulk

Mehmet Tekman, Wendi Bacon

Designing plasmids encoding predicted pathways by using the BASIC assembly method

Synthetic Biology

Kenza Bazi-Kabbaj, Thomas Duigou, Joan Hérisson, Guillaume Gricourt, Ioana Popescu, Jean-Loup Faulon

Visualization of RNA-Seq results with Volcano Plot

Transcriptomics

Maria Doyle

Biodiversity data exploration

Ecology

taxonomic data data quality

Olivier Norvez, Marie Josse, Coline Royaux, Yvan Le Bras

Workflow Reports

Using Galaxy and Managing your Data

workflows

Downloading and Deleting Data in Galaxy

Using Galaxy and Managing your Data

Simon Gladman, Helena Rasche

Microbial Variant Calling

Variant Analysis

prokaryote

Anna Syme, Simon Gladman, Torsten Seemann

Statistical analysis of DIA data

Proteomics

DIA

Matthias Fahrner, Melanie Föll

Differential abundance testing of small RNAs

Transcriptomics

Mallory Freeberg

Secretome Prediction

Proteomics

human

Florian Christoph Sigloch, Björn Grüning

Mapping Jobs to Destinations

Galaxy Server administration

ansible jobs git-gat

Nate Coraor, Björn Grüning, Helena Rasche

Debugging Galaxy

Development in Galaxy

Assunta DeSanto, John Davis, John Chilton

Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?

FAQ

Anna Syme, Simon Gladman

On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.

FAQ

Wendi Bacon, Mehmet Tekman

Training Infrastructure as a Service (TIaaS)

Galaxy Server administration

ansible training jobs git-gat

Helena Rasche, Saskia Hiltemann

RAD-Seq to construct genetic maps

Ecology

RAD-seq Genetic composition EBV class EBV dataset EBV workflow

Yvan Le Bras

Galaxy Admin Training Path

FAQ

Helena Rasche

Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools

Synthetic Biology

Guillaume Gricourt, Thomas Duigou, Kenza Bazi-Kabbaj, Joan Hérisson, Ioana Popescu, Jean-Loup Faulon

What is Taxonomy?

FAQ

Bérénice Batut

Annotating a protein list identified by LC-MS/MS experiments

Proteomics

DDA human

Valentin Loux, Florence Combes, David Christiany, Yves Vandenbrouck

Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

Epigenetics

ChIP-seq

Mallory Freeberg, Mo Heydarian, Vivek Bhardwaj, Joachim Wolff, Anika Erxleben

`docker-compose up` fails with error `/usr/bin/start.sh: line 133: /galaxy/.venv/bin/uwsgi: No such file or directory`

FAQ

Ross Lazarus

Visualization of RNA-Seq results with heatmap2

Transcriptomics

Maria Doyle

I want to use a collection for outputs but it always passes the test even when the script fails. Why?

FAQ

Ross Lazarus

First job I submitted remains grey or running for a long time - is it broken?

FAQ

Ross Lazarus

Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?

FAQ

Rahmot Afolabi

When I get a warning for base per sequence content, what should I do?

FAQ

Florian Heyl

Add genome and annotations to IGV from Galaxy

FAQ

Delphine Lariviere, Bérénice Batut, Helena Rasche, Saskia Hiltemann

Do you have resources to help me get started working in the cloud?

FAQ

Jon Trow, Adelaide Rhodes

Are these data free to use and download?

FAQ

Jon Trow, Adelaide Rhodes

How do I know what protocol my data was sequenced with?

FAQ

Wendi Bacon, Mehmet Tekman

Scripting Galaxy using the API and BioBlend

Development in Galaxy

jupyter-notebook

Distributed Object Storage

Galaxy Server administration

ansible storage

Nate Coraor, Helena Rasche, Gianmauro Cuccuru

When will aligned read objects be available for other data types?

FAQ

Jon Trow, Adelaide Rhodes

How do I know what I can do with a role? What variables are available?

FAQ

Helena Rasche, Nicola Soranzo, Simon Gladman

What is Gene Ontology (GO)?

FAQ

Florence Combes

What advantages does a Chromatogram Library have over a DDA-generated library or predicted spectral library?

FAQ

Emma Leith

My Rscript tool generates a strange R error on STDOUT about an invalid operation on a closure called 'args' ?

FAQ

Ross Lazarus

Genome Annotation

Genome Annotation

prokaryote work-in-progress

Anika Erxleben, Björn Grüning

Install tools via the Admin UI

FAQ

Saskia Hiltemann

Functional annotation of protein sequences

Genome Annotation

eukaryote

FASTQ format

FAQ

Bérénice Batut

Why do we use FASTQ interlacer and not the FASTQ joiner?

FAQ

Subina Mehta

Why does the query `SRR11772204 OR SRR11597145 OR SRR11667145` in the Run Selector not return any results?

FAQ

Anton Nekrutenko

My jobs are not running / I cannot see the history overview menu

FAQ

Rahmot Afolabi

External Authentication

Galaxy Server administration

authentication

Nate Coraor, Nicola Soranzo, Helena Rasche

Data source integration

Development in Galaxy

Bérénice Batut, Saskia Hiltemann, Gianmauro Cuccuru, Helena Rasche

UCSC - I fetched data from a remote website but now I’m logged out of Galaxy and my data is gone?

FAQ

Rahmot Afolabi

What is the difference between the roles with `role:` prefix and without?

FAQ

Helena Rasche

What kind of variants are seen in the output?

FAQ

Subina Mehta

Customising the welcome page

FAQ

Helena Rasche

Can RNA-seq techniques be applied to scRNA-seq?

FAQ

Wendi Bacon, Mehmet Tekman, Rahmot Afolabi

Operating system compatibility

FAQ

Helena Rasche

Searching Your History

Using Galaxy and Managing your Data

Helena Rasche, Anton Nekrutenko

What should I do special if on usegalaxy.be?

FAQ

Bert Droesbeke

Genome annotation with Prokka

Genome Annotation

prokaryote

Anna Syme, Torsten Seemann, Simon Gladman

Running more than one round of Pilon polishing

FAQ

Anna Syme, Simon Gladman

Example histories for the proteogenomics tutorials

FAQ

Subina Mehta

Are UMIs not actually unique?

FAQ

Wendi Bacon, Mehmet Tekman

Why is amplification more of an issue in scRNA-seq than RNA-seq?

FAQ

Wendi Bacon, Mehmet Tekman, Rahmot Afolabi

Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?

FAQ

Subina Mehta

Where can I read more about this analysis?

FAQ

Saskia Hiltemann

MSStats: what does ‘compare groups = yes’ mean? And the comparison matrix to define the contrast between the 2 groups?

FAQ

Melanie Föll

Can we polish the assembly with long reads too?

FAQ

Anna Syme, Simon Gladman

Can EncyclopeDIA be run on a DIA-MS dataset without a spectral library?

FAQ

Emma Leith

Error: "skipping: no hosts matched"

FAQ

Helena Rasche

RNAstar: Why do we set 36 for 'Length of the genomic sequence around annotated junctions'?

FAQ

Rahmot Afolabi

What does it mean to normalize the LFQ intensities?

FAQ

Melanie Föll

Why is Alevin is not working?

FAQ

Wendi Bacon, Mehmet Tekman

Why is Alevin is not working?

FAQ

Wendi Bacon, Mehmet Tekman

My snippy is running for a very long time. Is this normal?

FAQ

Peter van Heusden

Do I need to create collections to run MaxQuant analysis or can I use single sample inputs?

FAQ

Melanie Föll

I cannot run client tests because yarn is not installed.

FAQ

Saskia Hiltemann

JBrowse is taking a long time to complete?

FAQ

Saskia Hiltemann

Is it possible to subsample some samples if you have more reads?

FAQ

Lucille Delisle

Do you need to merge the databases? Because you can select multiple fasta files in MaxQuant.

FAQ

Melanie Föll

Why don't the aligned read files have quality scores?

FAQ

Jon Trow, Adelaide Rhodes

I have a really large search database, what search strategies do you recommend for searching my mass spectrometry dataset?

FAQ

Milla Berezutskaia

How many proteins can be identified and quantified in shotgun proteomics?

FAQ

Melanie Föll

Which search algorithms are recommended for searching the metaproteomics data?

FAQ

Milla Berezutskaia

Galaxy Monitoring with Reports

Galaxy Server administration

ansible monitoring git-gat

Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

What file/data formats are defined for I/O in Galaxy?

FAQ

Ross Lazarus

When is the "infer experiment" tool used in practice?

FAQ

Bérénice Batut

Add Mapped reads track to IGV from Galaxy

FAQ

Delphine Lariviere, Bérénice Batut, Saskia Hiltemann

Can I use alternative tools for the Quantification step?

FAQ

Cristóbal Gallardo

In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library?

FAQ

Lucille Delisle, Hans-Rudolf Hotz, Florian Heyl

Why does my assembly graph in Bandage look different to the one pictured in the tutorial?

FAQ

Anna Syme, Simon Gladman

Define once, reference many times

FAQ

Nate Coraor, Saskia Hiltemann

How many search engines can you use in SearchGUI?

FAQ

Subina Mehta

Flatten a list of list of paired datasets into a list of paired datasets

FAQ

Helena Rasche

How can I adapt this tutorial to my own data?

FAQ

Saskia Hiltemann

I have FASTQ files from metagenomics or metatranscriptomics datasets? How can I convert them into a protein FASTA file for metaproteomics searches?

FAQ

Milla Berezutskaia

16S Microbial Analysis with mothur (extended)

Metagenomics

Saskia Hiltemann, Bérénice Batut, Dave Clements

16S Microbial Analysis with mothur (short)

Metagenomics

Saskia Hiltemann, Bérénice Batut, Dave Clements

Why do I need that big (~5GB!) complicated Docker thing - can I just install the ToolFactory into our local galaxy server from the toolshed?

FAQ

Ross Lazarus

Is YAML sensitive to True/true/False/false

FAQ

Helena Rasche

The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda?

FAQ

Alex Ostrovsky, Dave B., Matthias Bernt

Where can I get planemo?

FAQ

Alex Ostrovsky, Dave B., Matthias Bernt

Do I have to run the tools in the order of the tutorial?

FAQ

Peter van Heusden

Where can I read more about Quality Control of data?

FAQ

Saskia Hiltemann

Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?

FAQ

Milla Berezutskaia

I’m using the same training data, tools, and parameters as the tutorial, but I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?

FAQ

Rahmot Afolabi

The UMAP Plots errors out sometimes?

FAQ

Wendi Bacon, Mehmet Tekman

What exactly is a ‘Gene profile’?

FAQ

Rahmot Afolabi

Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?

FAQ

Subina Mehta

I got slightly different numbers than were in the tutorial

FAQ

Rahmot Afolabi

What is the principle of an enrichment analysis?

FAQ

Florence Combes

MultiQC error for your FastQC reports?

FAQ

Saskia Hiltemann

AnnData Import/ AnnData Manipulate not working?

FAQ

Wendi Bacon, Mehmet Tekman

Including custom modifications into MaxQuant in Galaxy?

FAQ

Melanie Föll

I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?

FAQ

Mallory Freeberg

Contributing a Jupyter Notebook to the GTN

FAQ

Helena Rasche, Nicola Soranzo

Does MaxQuant give as output possibility the PSMs and PEPs?

FAQ

Melanie Föll

Is it possible to use alternative tools to those proposed in the tutorial?

FAQ

Wolfgang Maier

Is it possible to visualize the RNA STAR bam file using the JBrowse tool?

FAQ

Bérénice Batut

Automatically trim adapters (without providing custom sequences)

FAQ

Lucille Delisle, Hans-Rudolf Hotz, Florian Heyl

For the “quantitation method” what is the default if I just leave it as “None”? Label free?

FAQ

Melanie Föll

What is the advantage of breaking down protein to peptides before mass spec?

FAQ

Melanie Föll

What if you forget `--diff`?

FAQ

Helena Rasche

Variable connection

FAQ

Helena Rasche

Genome annotation with Maker

Genome Annotation

eukaryote

Anthony Bretaudeau

Genome annotation with Maker (short)

Genome Annotation

eukaryote

Anthony Bretaudeau

How does one convert RAW files to MGF peak lists within Galaxy?

FAQ

Milla Berezutskaia

What is a SNP?

FAQ

Saskia Hiltemann

Where can I find the full listing and description of the columns in each metadata table?

FAQ

Jon Trow, Adelaide Rhodes

Metatranscriptomics analysis using microbiome RNA-seq data

Metagenomics

metatranscriptomics

Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar, Saskia Hiltemann

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Metagenomics

metatranscriptomics

Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar, Saskia Hiltemann

UCSC import: what should my file look like?

FAQ

Lucille Delisle, Hans-Rudolf Hotz, Florian Heyl

Changing the heatmap colours

FAQ

Lucille Delisle, Hans-Rudolf Hotz, Florian Heyl

How many mules?

FAQ

Helena Rasche, Saskia Hiltemann

When can you use (or cannot use) Match between runs in MaxQuant?

FAQ

Melanie Föll

Are Barcodes always on R1 and Sequence data on R2?

FAQ

Wendi Bacon, Mehmet Tekman

In 'infer experiments' I get unequal numbers, but in the IGV it looks like it is unstranded. What does this mean?

FAQ

Bérénice Batut