Search Tutorials

Creating Galaxy tools from Conda Through Deployment

Development in Galaxy

Alex Ostrovsky, Dave B., Matthias Bernt

Use Jupyter notebooks in Galaxy

Using Galaxy and Managing your Data

Delphine Lariviere

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

FAQ

Ross Lazarus

ToolFactory: Generating Tools From More Complex Scripts

Development in Galaxy

Ross Lazarus

Only one Planemo test runs at a time. Why doesn't the server allow more than one at once?

FAQ

Ross Lazarus

ToolFactory: Generating Tools From Simple Scripts

Development in Galaxy

Ross Lazarus, Helena Rasche

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

Deploying a compute cluster in OpenStack via Terraform

Galaxy Server administration

terraform deploying cloud

Helena Rasche

Galaxy Monitoring with gxadmin

Galaxy Server administration

monitoring ansible git-gat

Helena Rasche

How I learned to stop worrying and love the systemd

Galaxy Server administration

ansible systemd

Small Non-coding RNA Clustering using BlockClust

Transcriptomics

Pavankumar Videm

Galaxy Installation with Ansible

Galaxy Server administration

ansible deploying git-gat

Data Manipulation Olympics

Introduction to Galaxy Analyses

cyoa

Automation with Jenkins

Galaxy Server administration

ansible automation

Helena Rasche

Unicycler Assembly

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Simon Gladman

Clustering 3K PBMCs with Scanpy

Transcriptomics

single-cell 10x

Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman

Differential abundance testing of small RNAs

Transcriptomics

Mallory Freeberg

Reference-based RNAseq data analysis (long)

Transcriptomics

work-in-progress

Anton Nekrutenko

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

Variant Analysis

covid19

Wolfgang Maier, Bérénice Batut

Mass spectrometry: LC-MS analysis

Metabolomics

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

High Throughput Molecular Dynamics and Analysis

Computational chemistry

Simon Bray, Tharindu Senapathi, Christopher Barnett, Björn Grüning

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

Assembly

covid19

Wolfgang Maier

Reference Data with CVMFS without Ansible

Galaxy Server administration

Simon Gladman, Helena Rasche

Mass spectrometry: LC-MS data processing

Metabolomics

Mélanie Petera, Workflow4Metabolomics core team

Trajectory Analysis using Monocle3

Transcriptomics

single-cell trajectory-analysis paper-replication

MaxQuant and MSstats for the analysis of label-free data

Proteomics

label-free

Melanie Föll, Matthias Fahrner

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

Statistics and machine learning

Kaivan Kamali

NGS data logistics

Introduction to Galaxy Analyses

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

Peptide Library Data Analysis

Proteomics

Jayadev Joshi, Daniel Blankenberg

Mass spectrometry: LC-MS preprocessing with XCMS

Metabolomics

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

Network analysis with Heinz

Transcriptomics

metatranscriptomics network analysis

Chao (Cico) Zhang

Reference Data with CVMFS

Galaxy Server administration

ansible git-gat

Simon Gladman, Helena Rasche

InterMine integration with Galaxy

Using Galaxy and Managing your Data

Daniela Butano, Yo Yehudi

Image classification in Galaxy with fruit 360 dataset

Statistics and machine learning

Kaivan Kamali

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

Computational chemistry

Aurélien F. A. Moumbock, Simon Bray

Mass spectrometry imaging: Loading and exploring MSI data

Proteomics

mouse imaging

Melanie Föll, Björn Grüning

Pre-processing of 10X Single-Cell RNA Datasets

Transcriptomics

single-cell 10x

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

VGP assembly pipeline

Assembly

pacbio eukaryote VGP

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

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

Microbial Variant Calling

Variant Analysis

prokaryote

Anna Syme, Simon Gladman, Torsten Seemann

Making sense of a newly assembled genome

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Helena Rasche

Genome Annotation

Genome Annotation

prokaryote work-in-progress

Anika Erxleben, Björn Grüning

Introduction to Genomics and Galaxy

Introduction to Galaxy Analyses

Dave Clements, Cristóbal Gallardo

Galaxy Interactive Tools

Development in Galaxy

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

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

Using Galaxy and Managing your Data

ncbi covid19

Jon Trow, Adelaide Rhodes

Antibiotic resistance detection

Metagenomics

nanopore plasmids assembly amr

Willem de Koning, Saskia Hiltemann

CRISPR screen analysis

Genome Annotation

genome editing CRISPR essential genes cell line

Maria Doyle, Kenji Fujihara, Twishi Gulati

Visualisation with Circos

Visualisation

Saskia Hiltemann, Helena Rasche, Cristóbal Gallardo

Galaxy Interactive Tools

Galaxy Server administration

ansible interactive-tools

Nate Coraor, Simon Gladman, Helena Rasche, Anthony Bretaudeau

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

FAQ

Alex Ostrovsky, Dave B., Matthias Bernt

Species distribution modeling

Ecology

interactive-tools

Elisa Michon, Yvan Le Bras, Bérénice Batut

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

Metagenomics

nanopore beer citizen science metagenomics

Calling variants in non-diploid systems

Variant Analysis

prokaryote

Anton Nekrutenko, Alex Ostrovsky

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

Writing Automated Tests for Galaxy

Development in Galaxy

John Davis, John Chilton

RNA-Seq analysis with AskOmics Interactive Tool

Transcriptomics

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

Generating a single cell matrix using Alevin

Transcriptomics

single-cell 10x paper-replication español

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

Refining Genome Annotations with Apollo (eukaryotes)

Genome Annotation

eukaryote cyoa

Anthony Bretaudeau, Erasmus+ Programme

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

Transcriptomics

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

ATAC-Seq data analysis

Epigenetics

Lucille Delisle, Maria Doyle, Florian Heyl

Exome sequencing data analysis for diagnosing a genetic disease

Variant Analysis

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

Automating Galaxy workflows using the command line

Using Galaxy and Managing your Data

workflows variant-analysis covid19

Simon Bray, Wolfgang Maier

Refining Genome Annotations with Apollo (prokaryotes)

Genome Annotation

prokaryote

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

Mass spectrometry imaging: Examining the spatial distribution of analytes

Metabolomics

Melanie Föll, Maren Stillger

Genome Assembly of MRSA using Oxford Nanopore MinION Data

Assembly

nanopore assembly amr

VGP assembly pipeline - short version

Assembly

pacbio eukaryote VGP

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

Analyses of metagenomics data - The global picture

Metagenomics

Saskia Hiltemann, Bérénice Batut

Submitting sequence data to ENA

Using Galaxy and Managing your Data

covid19

Miguel Roncoroni, Bert Droesbeke

Tree thinking for tuberculosis evolution and epidemiology

Evolution

prokaryotes phylogenetics evolution work-in-progress

Christoph Stritt, Daniela Brites, Galo A. Goig

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Proteomics

DDA SILAC

Florian Christoph Sigloch, Björn Grüning, Matthias Fahrner

Using dataset collections

Using Galaxy and Managing your Data

collections

Anton Nekrutenko

Genome Assembly of MRSA using Illumina MiSeq Data

Assembly

illumina assembly amr

Connecting Galaxy to a compute cluster

Galaxy Server administration

jobs ansible git-gat

Nate Coraor, Björn Grüning, Helena Rasche

From small to large-scale genome comparison

Genome Annotation

Esteban Perez-Wohlfeil

Introduction to Machine Learning using R

Statistics and machine learning

interactive-tools

Fotis E. Psomopoulos, Erasmus+ Programme

Mass spectrometry imaging: Finding differential analytes

Metabolomics

Melanie Föll

M. tuberculosis Variant Analysis

Variant Analysis

prokaryote

Peter van Heusden, Simon Gladman, Thoba Lose

Protein-ligand docking

Computational chemistry

Simon Bray

Genome annotation with Funannotate

Genome Annotation

eukaryote

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Epigenetics

Joachim Wolff, Fidel Ramirez, Vivek Bhardwaj, Ekaterina Polkh

Age prediction using machine learning

Statistics and machine learning

Ekaterina Polkh, Anup Kumar

Contributing to BioBlend as a developer

Development in Galaxy

Erik Schill, Simon Bray

Galaxy Monitoring with Telegraf and Grafana

Galaxy Server administration

ansible monitoring git-gat

Helena Rasche

Downstream Single-cell RNA analysis with RaceID

Transcriptomics

single-cell

Mehmet Tekman, Alex Ostrovsky

Galaxy 101 for everyone

Introduction to Galaxy Analyses

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

16S Microbial analysis with Nanopore data

Metagenomics

nanopore

Cristóbal Gallardo

Essential genes detection with Transposon insertion sequencing

Genome Annotation

bacteria tnseq essential genes

Delphine Lariviere, Bérénice Batut

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

Computational chemistry

covid19

Simon Bray

metaQuantome 1: Data creation

Proteomics

microbiome

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

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

Transcriptomics

Florian Heyl, Daniel Maticzka, Bérénice Batut

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

1: RNA-Seq reads to counts

Transcriptomics

collections mouse QC

Maria Doyle, Belinda Phipson, Harriet Dashnow

metaQuantome 2: Function

Proteomics

microbiome

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

Pre-processing of Single-Cell RNA Data

Transcriptomics

single-cell

Mehmet Tekman, Bérénice Batut, Anika Erxleben, Wolfgang Maier

Analysis of plant scRNA-Seq Data with Scanpy

Transcriptomics

single-cell plants paper-replication

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

MaxQuant and MSstats for the analysis of TMT data

Proteomics

DDA TMT

Klemens Fröhlich, Melanie Föll, Matthias Fahrner

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

Identifying tuberculosis transmission links: from SNPs to transmission clusters

Evolution

work-in-progress

Galo A. Goig, Daniela Brites, Christoph Stritt

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

Variant Analysis

Wolfgang Maier

Ansible

Galaxy Server administration

ansible

Helena Rasche, Saskia Hiltemann

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Variant Analysis

cancer cyoa

Jasper Ouwerkerk, Wolfgang Maier, Helena Rasche, Saskia Hiltemann

Compute and analyze biodiversity metrics with PAMPA toolsuite

Ecology

Coline Royaux, Yvan Le Bras, Jean-Baptiste Mihoub

RNA-RNA interactome data analysis

Transcriptomics

Pavankumar Videm

3: RNA-seq genes to pathways

Transcriptomics

mouse

Maria Doyle, Belinda Phipson

Whole transcriptome analysis of Arabidopsis thaliana

Transcriptomics

miRNA plants

Cristóbal Gallardo, Pavankumar Videm, Beatriz Serrano-Solano

Quality Control

Sequence analysis

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

Machine Learning Modeling of Anticancer Peptides

Proteomics

ML cancer

Jayadev Joshi, Daniel Blankenberg

metaQuantome 3: Taxonomy

Proteomics

microbiome

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

Multisample Analysis

Using Galaxy and Managing your Data

collections

Anton Nekrutenko, Anne Pajon

Generic plugins

Development in Galaxy

Saskia Hiltemann, Youri Hoogstrate

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Climate

interactive-tools

Anne Fouilloux, Hui Tang

Regional GAM

Ecology

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

Long non-coding RNAs (lncRNAs) annotation with FEELnc

Genome Annotation

eukaryote

GO Enrichment Analysis

Transcriptomics

IGC Bioinformatics Unit, Maria Doyle

Understanding Barcodes

Transcriptomics

single-cell

Mehmet Tekman

Getting your hands-on climate data

Climate

Anne Fouilloux

RStudio in Galaxy

Using Galaxy and Managing your Data

interactive-tools

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

Calling variants in diploid systems

Variant Analysis

Anton Nekrutenko, Nicola Soranzo

Comparative gene analysis in unannotated genomes

Genome Annotation

evolution annotation vgp cookbook eukaryote prokaryote

Anton Nekrutenko

De novo transcriptome reconstruction with RNA-Seq

Transcriptomics

Mallory Freeberg, Mo Heydarian

Visualization of RNA-Seq results with Volcano Plot in R

Transcriptomics

interactive-tools

Maria Doyle

Mapping and molecular identification of phenotype-causing mutations

Variant Analysis

Wolfgang Maier

Biomarker candidate identification

Proteomics

DDA human

Florence Combes, David Christiany, Valentin Loux, Yves Vandenbrouck

Running more than one round of Pilon polishing

FAQ

Anna Syme, Simon Gladman

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

Genomic Data Visualisation with JBrowse

Visualisation

Helena Rasche, Saskia Hiltemann, Erasmus+ Programme

Bulk RNA Deconvolution with MuSiC

Transcriptomics

single-cell mouse human deconvolution bulk

Mehmet Tekman, Wendi Bacon

RNA Seq Counts to Viz in R

Transcriptomics

interactive-tools

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

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

Statistics and machine learning

Kaivan Kamali

Formation of the Super-Structures on the Inactive X

Epigenetics

ChIP-seq

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

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

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

Statistics and machine learning

Kaivan Kamali

Text-mining with the SimText toolset

Statistics and machine learning

interactive-tools

Marie Gramm, Dennis Lal group, Daniel Blankenberg

Metabarcoding/eDNA through Obitools

Ecology

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

Creating, Editing and Importing Galaxy Workflows

Using Galaxy and Managing your Data

workflows

Marius van den Beek

Mapping Jobs to Destinations

Galaxy Server administration

ansible jobs git-gat

Nate Coraor, Björn Grüning, Helena Rasche

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

Proteomics

DDA human

Valentin Loux, Florence Combes, David Christiany, Yves Vandenbrouck

Genome annotation with Prokka

Genome Annotation

prokaryote

Anna Syme, Torsten Seemann, Simon Gladman

Contributing a New Feature to Galaxy Core

Development in Galaxy

John Chilton, John Davis

Debugging Galaxy

Development in Galaxy

Assunta DeSanto, John Davis, John Chilton

Classification in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

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

Climate

interactive-tools

Anne Fouilloux

Inferring Trajectories using Python (Jupyter Notebook) in Galaxy

Transcriptomics

single-cell 10x paper-replication interactive-tools

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

Galaxy Database schema

Galaxy Server administration

Hans-Rudolf Hotz, Björn Grüning

Mass spectrometry : GC-MS analysis with metaMS package

Metabolomics

work-in-progress

Julien Saint-Vanne

Regression in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

De novo transcriptome assembly, annotation, and differential expression analysis

Transcriptomics

work-in-progress

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

Clustering in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar

Infinium Human Methylation BeadChip

Epigenetics

Katarzyna Murat, Krzysztof Poterlowicz

EncyclopeDIA

Proteomics

DIA

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

Managing Galaxy on Kubernetes

Galaxy Server administration

kubernetes

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

Calling very rare variants

Variant Analysis

work-in-progress

Anton Nekrutenko, Nick Stoler

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

An Introduction to Genome Assembly

Assembly

Simon Gladman

Biodiversity data exploration

Ecology

Olivier Norvez, Marie, Coline Royaux, Yvan Le Bras

Label-free data analysis using MaxQuant

Proteomics

DDA label-free

Melanie Föll, Matthias Fahrner

Nucleoli segmentation and feature extraction using CellProfiler

Imaging

Beatriz Serrano-Solano, Jean-Karim Hériché

Understanding Galaxy history system

Using Galaxy and Managing your Data

Anton Nekrutenko, Martin Čech, Helena Rasche

IGV Introduction

Introduction to Galaxy Analyses

Anton Nekrutenko, Joachim Wolff, Anne Pajon

Galaxy 101

Introduction to Galaxy Analyses

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

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

Proteomics

Florian Christoph Sigloch, Björn Grüning

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

Sequence analysis

covid19

Wolfgang Maier

How to reproduce published Galaxy analyses

Introduction to Galaxy Analyses

Melanie Föll, Anne Fouilloux

Combining datasets after pre-processing

Transcriptomics

single-cell 10x paper-replication español

From peaks to genes

Introduction to Galaxy Analyses

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

Secretome Prediction

Proteomics

human

Florian Christoph Sigloch, Björn Grüning

Single-cell quality control with scater

Transcriptomics

single-cell

Graham Etherington, Nicola Soranzo

Somatic Variant Discovery from WES Data Using Control-FREEC

Variant Analysis

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

Peptide and Protein ID using OpenMS tools

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Visualization of RNA-Seq results with Volcano Plot

Transcriptomics

Maria Doyle

Genome assembly using PacBio data

Assembly

assembly pacbio

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

Distributed Object Storage

Galaxy Server administration

ansible storage

Nate Coraor, Helena Rasche, Gianmauro Cuccuru

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

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Library Generation for DIA Analysis

Proteomics

DIA

Matthias Fahrner, Melanie Föll

Introduction to deep learning

Statistics and machine learning

Anup Kumar, Alireza Khanteymoori

Proteogenomics 1: Database Creation

Proteomics

proteogenomics

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

Object tracking using CellProfiler

Imaging

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

What is Taxonomy?

FAQ

Bérénice Batut

Galaxy Webhooks

Development in Galaxy

Clemens Blank, Martin Čech, Björn Grüning

Upgrading Galaxy

Galaxy Server administration

ansible

Simon Gladman

De Bruijn Graph Assembly

Assembly

Simon Gladman, Helena Rasche, Saskia Hiltemann

Which icons are available to use in my tutorial?

FAQ

Saskia Hiltemann

Genome Assembly Quality Control

Assembly

assembly quality control

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

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

Running molecular dynamics simulations using GROMACS

Computational chemistry

Simon Bray

JavaScript plugins

Development in Galaxy

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

Machine learning: classification and regression

Statistics and machine learning

Anup Kumar, Bérénice Batut

Visualize Climate data with Panoply netCDF viewer

Climate

interactive-tools

Anne Fouilloux

Mapping

Sequence analysis

Joachim Wolff, Bérénice Batut, Helena Rasche

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

FAQ

Jon Trow, Adelaide Rhodes

Visualization of RNA-Seq results with heatmap2

Transcriptomics

Maria Doyle

Setting up molecular systems

Computational chemistry

Christopher Barnett, Simon Bray, Nadia Goué

External Authentication

Galaxy Server administration

authentication

Nate Coraor, Nicola Soranzo, Helena Rasche

Training Infrastructure as a Service (TIaaS)

Galaxy Server administration

ansible training jobs git-gat

Helena Rasche, Saskia Hiltemann

Pangeo Notebook in Galaxy - Introduction to Xarray

Climate

pangeo interactive-tools jupyter-notebook jupyter-notebook

Anne Fouilloux

Galaxy Installation on Kubernetes

Galaxy Server administration

kubernetes

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

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

Peptide and Protein ID using SearchGUI and PeptideShaker

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Extracting Workflows from Histories

Using Galaxy and Managing your Data

workflows

Dave Clements

DIA Analysis using OpenSwathWorkflow

Proteomics

DIA

Matthias Fahrner, Melanie Föll

What exactly is a ‘Gene profile’?

FAQ

Rahmot Afolabi

Analyse HeLa fluorescence siRNA screen

Imaging

Thomas Wollmann

Data Libraries

Galaxy Server administration

ansible storage git-gat

Helena Rasche, Saskia Hiltemann

JupyterLab in Galaxy

Using Galaxy and Managing your Data

interactive-tools

Masking repeats with RepeatMasker

Genome Annotation

eukaryote

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

Proteogenomics 3: Novel peptide analysis

Proteomics

proteogenomics

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

RAD-Seq de-novo data analysis

Ecology

RAD-seq

Yvan Le Bras

Rule Based Uploader

Using Galaxy and Managing your Data

collections tags

John Chilton, Helena Rasche

Preparing genomic data for phylogeny reconstruction

Ecology

Miguel Roncoroni, Brigida Gallone

Enable upload via FTP

Galaxy Server administration

data git-gat

Lucille Delisle

Chloroplast genome assembly

Assembly

plants nanopore

Anna Syme

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

FAQ

Wendi Bacon, Mehmet Tekman, Rahmot Afolabi

RAD-Seq Reference-based data analysis

Ecology

RAD-seq

Yvan Le Bras

Visualization of RNA-Seq results with CummeRbund

Transcriptomics

Andrea Bagnacani

Running molecular dynamics simulations using NAMD

Computational chemistry

work-in-progress

Christopher Barnett, Tharindu Senapathi, Simon Bray

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

FAQ

Emma Leith

Deploying Wireguard for private mesh networking

Galaxy Server administration

wireguard networking

Proteogenomics 2: Database Search

Proteomics

proteogenomics

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

A short introduction to Galaxy

Introduction to Galaxy Analyses

español

Anna Syme, Nicola Soranzo

How to read a Diff

FAQ

Helena Rasche

Downloading and Deleting Data in Galaxy

Using Galaxy and Managing your Data

Simon Gladman, Helena Rasche

Deploying Tailscale/Headscale for private mesh networking

Galaxy Server administration

wireguard networking

Operating system compatibility

FAQ

Helena Rasche

Rule Based Uploader: Advanced

Using Galaxy and Managing your Data

collections tags

John Chilton, Helena Rasche

Using Workflow Parameters

Using Galaxy and Managing your Data

workflows

Marius van den Beek, Helena Rasche

Protein FASTA Database Handling

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Scripting Galaxy using the API and BioBlend

Development in Galaxy

jupyter-notebook

Which search algorithms are recommended for searching the metaproteomics data?

FAQ

Milla Berezutskaia

Interval-Wise Testing for omics data

Statistics and machine learning

Marzia A Cremona, Fabio Cumbo

RAD-Seq to construct genetic maps

Ecology

RAD-seq

Yvan Le Bras

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

FAQ

Melanie Föll

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

FAQ

Anton Nekrutenko

Name tags for following complex histories

Using Galaxy and Managing your Data

Helena Rasche

Data source integration

Development in Galaxy

Bérénice Batut, Saskia Hiltemann, Gianmauro Cuccuru, Helena Rasche

Analysis of molecular dynamics simulations

Computational chemistry

Christopher Barnett, Tharindu Senapathi, Simon Bray, Nadia Goué

Define once, reference many times

FAQ

Nate Coraor, Saskia Hiltemann

Can we polish the assembly with long reads too?

FAQ

Anna Syme, Simon Gladman

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

How to Contribute to Galaxy

FAQ

John Chilton, Helena Rasche

Galaxy Tool Management with Ephemeris

Galaxy Server administration

tools git-gat

Martin Čech, Helena Rasche, Nicola Soranzo

Metaproteomics tutorial

Proteomics

microbiome

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

The input for a tool is not listed in the dropdown

FAQ

Saskia Hiltemann

What is the principle of an enrichment analysis?

FAQ

Florence Combes

My Galaxy looks different than in the tutorial/video

FAQ

Rahmot Afolabi

Do we need a contaminant FASTA for MQ in galaxy?

FAQ

Melanie Föll

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

Workflow Reports

Using Galaxy and Managing your Data

workflows

Group tags for complex experimental designs

Using Galaxy and Managing your Data

Marius van den Beek

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

FAQ

Anna Syme, Simon Gladman

I can’t find the “Analyze Data” button

FAQ

Rahmot Afolabi

Statistical analysis of DIA data

Proteomics

DIA

Matthias Fahrner, Melanie Föll

Introduction to image analysis using Galaxy

Imaging

Thomas Wollmann, Saskia Hiltemann

How does one compare metaproteomics measurements from two experimental conditions?

FAQ

Milla Berezutskaia

FASTQ format

FAQ

Bérénice Batut

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Climate

pangeo

Anne Fouilloux

What is Gene Ontology (GO)?

FAQ

Florence Combes

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

FAQ

Bérénice Batut

What should I do special if on usegalaxy.be?

FAQ

Bert Droesbeke

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

FAQ

Jon Trow, Adelaide Rhodes

Customising the welcome page

FAQ

Helena Rasche

Use Singularity containers for running Galaxy jobs

Galaxy Server administration

jobs ansible git-gat

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

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

FAQ

Melanie Föll

How many search engines can you use in SearchGUI?

FAQ

Subina Mehta

DNA Methylation data analysis

Epigenetics

Joachim Wolff, Devon Ryan

The UMAP Plots errors out sometimes?

FAQ

Wendi Bacon, Mehmet Tekman

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

FAQ

Helena Rasche, Nicola Soranzo, Simon Gladman

Metatranscriptomics analysis using microbiome RNA-seq data

Metagenomics

metatranscriptomics

Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar, 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 (short)

Metagenomics

metatranscriptomics

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

JBrowse is taking a long time to complete?

FAQ

Saskia Hiltemann

Where can I get planemo?

FAQ

Alex Ostrovsky, Dave B., Matthias Bernt

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

Functional annotation of protein sequences

Genome Annotation

eukaryote

Basics of machine learning

Statistics and machine learning

Anup Kumar

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

FAQ

Ross Lazarus

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

FAQ

Melanie Föll

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

FAQ

Rahmot Afolabi

Are these data free to use and download?

FAQ

Jon Trow, Adelaide Rhodes

Why do we only consider highly variable genes?

FAQ

Rahmot Afolabi

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

FAQ

Peter van Heusden

Running Ansible on your remote machine

FAQ

Helena Rasche

Variable connection

FAQ

Helena Rasche

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

FAQ

Jon Trow, Adelaide Rhodes

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

FAQ

Wendi Bacon, Mehmet Tekman, Rahmot Afolabi

Searching Your History

Using Galaxy and Managing your Data

Helena Rasche, Anton Nekrutenko

Changing the heatmap colours

FAQ

Lucille Delisle, Hans-Rudolf Hotz, Florian Heyl

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

FAQ

Wendi Bacon, Mehmet Tekman

Why do we have a variant mapping file when it is not being used in the workflow?

FAQ

Subina Mehta

Additional resources to learn more about proteomic data analysis

FAQ

Melanie Föll

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

FAQ

Emma Leith

Got lost along the way?

FAQ

Helena Rasche

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

FAQ

Bérénice Batut

What if you forget `--diff`?

FAQ

Helena Rasche

Where can I find example queries for use in the cloud and elsewhere?

FAQ

Jon Trow, Adelaide Rhodes

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

FAQ

Subina Mehta

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

FAQ

Helena Rasche

Add genome and annotations to IGV from Galaxy

FAQ

Delphine Lariviere, Bérénice Batut, Helena Rasche, Saskia Hiltemann

Galaxy Admin Training Path

FAQ

Helena Rasche

What does it mean to normalize the LFQ intensities?

FAQ

Melanie Föll

Can this ASaiM workflow be used for single-end data?

FAQ

Subina Mehta

Add Mapped reads track to IGV from Galaxy

FAQ

Delphine Lariviere, Bérénice Batut, Saskia Hiltemann

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

FAQ

Milla Berezutskaia

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

FAQ

Lucille Delisle

Can I use these workflows on datasets generated from our laboratory?

FAQ

Milla Berezutskaia

Can I use these workflows on datasets generated from our laboratory?

FAQ

Subina Mehta

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

FAQ

Wendi Bacon, Mehmet Tekman

Galaxy Monitoring with Reports

Galaxy Server administration

ansible monitoring git-gat

Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

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

FAQ

Rahmot Afolabi

It says I already have an account when registering for ecology.usegalaxy.eu

FAQ

Coline Royaux, Yvan Le Bras

How many mules?

FAQ

Helena Rasche, Saskia Hiltemann

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

Can I use alternative tools for the Quantification step?

FAQ

Cristóbal Gallardo

What kind of variants are seen in the output?

FAQ

Subina Mehta

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

FAQ

Rahmot Afolabi

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

FAQ

Ross Lazarus

Including custom modifications into MaxQuant in Galaxy?

FAQ

Melanie Föll

Is the ToolFactory a complete replacement for manual tool building?

FAQ

Ross Lazarus

Install tools via the Admin UI

FAQ

Saskia Hiltemann

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

FAQ

Peter van Heusden

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

FAQ

Subina Mehta

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

FAQ

Florian Heyl

Genome annotation with Maker

Genome Annotation

eukaryote

Anthony Bretaudeau

Genome annotation with Maker (short)

Genome Annotation

eukaryote

Anthony Bretaudeau

If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide).

FAQ

Melanie Föll

The tutorial uses the normalised count table for visualisation. What about using VST normalised counts or rlog normalised counts?

FAQ

Bérénice Batut

How can I adapt this tutorial to my own data?

FAQ

Saskia Hiltemann

What is a SNP?

FAQ

Saskia Hiltemann

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

FAQ

Melanie Föll

Where can I read more about this analysis?

FAQ

Saskia Hiltemann

Downloading the files from the NCBI server fails or takes too long.

FAQ

Wolfgang Maier

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

FAQ

Subina Mehta

The Build tissue-specific expression dataset tool (step one) exits with an error code.

FAQ

Florence Combes

Does MaxQuant give as output possibility the PSMs and PEPs?

FAQ

Melanie Föll

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

FAQ

Bérénice Batut

Can we use the ASaiM-MT workflow on multiple input files at the same time?

FAQ

Subina Mehta

UCSC import: what should my file look like?

FAQ

Lucille Delisle, Hans-Rudolf Hotz, Florian Heyl

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

FAQ

Melanie Föll

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

FAQ

Ross Lazarus

Example histories for the proteogenomics tutorials

FAQ

Subina Mehta

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

FAQ

Milla Berezutskaia