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Unicycler Assembly

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Simon Gladman

Chloroplast genome assembly

Assembly

plants nanopore

Anna Syme

De Bruijn Graph Assembly

Assembly

Simon Gladman, Helena Rasche, Saskia Hiltemann

An Introduction to Genome Assembly

Assembly

Simon Gladman

Genome assembly using PacBio data

Assembly

assembly pacbio

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

VGP assembly pipeline

Assembly

pacbio eukaryote VGP

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

Genome Assembly Quality Control

Assembly

assembly quality control

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

VGP assembly pipeline - short version

Assembly

pacbio eukaryote VGP

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

Genome Assembly of MRSA using Illumina MiSeq Data

Assembly

illumina assembly amr

Genome Assembly of MRSA using Oxford Nanopore MinION Data

Assembly

nanopore assembly amr

Making sense of a newly assembled genome

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Helena Rasche

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

Assembly

covid19

Wolfgang Maier

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

Antibiotic resistance detection

Metagenomics

nanopore plasmids assembly amr

Willem de Koning, Saskia Hiltemann

Long non-coding RNAs (lncRNAs) annotation with FEELnc

Genome Annotation

eukaryote

Masking repeats with RepeatMasker

Genome Annotation

eukaryote

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

Can we polish the assembly with long reads too?

FAQ

Anna Syme, Simon Gladman

De novo transcriptome assembly, annotation, and differential expression analysis

Transcriptomics

work-in-progress

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

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

FAQ

Anna Syme, Simon Gladman

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

Comparative gene analysis in unannotated genomes

Genome Annotation

evolution annotation vgp cookbook eukaryote prokaryote

Anton Nekrutenko

Proteogenomics 1: Database Creation

Proteomics

proteogenomics

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

Preparing genomic data for phylogeny reconstruction

Ecology

phylogeny data handling functional annotation

Miguel Roncoroni, Brigida Gallone

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

Using Galaxy and Managing your Data

ncbi covid19

Jon Trow, Adelaide Rhodes

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

Genome annotation with Funannotate

Genome Annotation

eukaryote

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

Reference-based RNAseq data analysis (long)

Transcriptomics

work-in-progress

Anton Nekrutenko

Galaxy Monitoring with gxadmin

Galaxy Server administration

monitoring ansible git-gat

Helena Rasche

Calling variants in non-diploid systems

Variant Analysis

prokaryote

Anton Nekrutenko, Alex Ostrovsky

Running more than one round of Pilon polishing

FAQ

Anna Syme, Simon Gladman

Genome annotation with Prokka

Genome Annotation

prokaryote

Anna Syme, Torsten Seemann, Simon Gladman

De novo transcriptome reconstruction with RNA-Seq

Transcriptomics

Mallory Freeberg, Mo Heydarian

RAD-Seq de-novo data analysis

Ecology

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

Yvan Le Bras

Object tracking using CellProfiler

Imaging

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

From small to large-scale genome comparison

Genome Annotation

Esteban Perez-Wohlfeil

Introduction to Genomics and Galaxy

Introduction to Galaxy Analyses

Dave Clements, Cristóbal Gallardo

Nucleoli segmentation and feature extraction using CellProfiler

Imaging

Beatriz Serrano-Solano, Jean-Karim Hériché

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

Computational chemistry

covid19

Simon Bray

Classification in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Climate

interactive-tools

Anne Fouilloux, Hui Tang

Protein-ligand docking

Computational chemistry

Simon Bray

Label-free data analysis using MaxQuant

Proteomics

DDA label-free

Melanie Föll, Matthias Fahrner

Submitting sequence data to ENA

Using Galaxy and Managing your Data

covid19

Miguel Roncoroni, Bert Droesbeke

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

Climate

interactive-tools

Anne Fouilloux

High Throughput Molecular Dynamics and Analysis

Computational chemistry

Simon Bray, Tharindu Senapathi, Christopher Barnett, Björn Grüning

Refining Genome Annotations with Apollo (prokaryotes)

Genome Annotation

prokaryote

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

Understanding Galaxy history system

Using Galaxy and Managing your Data

Anton Nekrutenko, Martin Čech, Helena Rasche

1: RNA-Seq reads to counts

Transcriptomics

collections mouse QC

Maria Doyle, Belinda Phipson, Harriet Dashnow

Quality Control

Sequence analysis

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

Ansible

Galaxy Server administration

ansible

Helena Rasche, Saskia Hiltemann

Galaxy Installation with Ansible

Galaxy Server administration

ansible deploying git-gat

Visualisation with Circos

Visualisation

Saskia Hiltemann, Helena Rasche, Cristóbal Gallardo

Writing Automated Tests for Galaxy

Development in Galaxy

John Davis, John Chilton

Reference Data with CVMFS

Galaxy Server administration

ansible git-gat

Simon Gladman, Helena Rasche

Upgrading Galaxy

Galaxy Server administration

ansible

Simon Gladman

Contributing a New Feature to Galaxy Core

Development in Galaxy

John Chilton, John Davis

Automation with Jenkins

Galaxy Server administration

ansible automation

Helena Rasche

Distributed Object Storage

Galaxy Server administration

ansible storage

Nate Coraor, Helena Rasche, Gianmauro Cuccuru

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

Generating a single cell matrix using Alevin

Transcriptomics

single-cell 10x paper-replication español

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

FAQ

Subina Mehta

Galaxy Monitoring with Telegraf and Grafana

Galaxy Server administration

ansible monitoring git-gat

Helena Rasche

Getting your hands-on climate data

Climate

Anne Fouilloux

Clustering 3K PBMCs with Scanpy

Transcriptomics

single-cell 10x

Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman

Understanding Barcodes

Transcriptomics

single-cell

Mehmet Tekman

Running molecular dynamics simulations using NAMD

Computational chemistry

work-in-progress

Christopher Barnett, Tharindu Senapathi, Simon Bray

Error: "skipping: no hosts matched"

FAQ

Helena Rasche

Calling very rare variants

Variant Analysis

work-in-progress

Anton Nekrutenko, Nick Stoler

Galaxy Interactive Tools

Galaxy Server administration

ansible interactive-tools

Nate Coraor, Simon Gladman, Helena Rasche, Anthony Bretaudeau

Enable upload via FTP

Galaxy Server administration

data git-gat

Lucille Delisle

Reference Data with CVMFS without Ansible

Galaxy Server administration

Simon Gladman, 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

Tree thinking for tuberculosis evolution and epidemiology

Evolution

prokaryotes phylogenetics evolution work-in-progress

Christoph Stritt, Daniela Brites, Galo A. Goig

Running Ansible on your remote machine

FAQ

Helena Rasche

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

Proteomics

DDA human

Valentin Loux, Florence Combes, David Christiany, Yves Vandenbrouck

Galaxy Monitoring with Reports

Galaxy Server administration

ansible monitoring git-gat

Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche

Running molecular dynamics simulations using GROMACS

Computational chemistry

Simon Bray

Pre-processing of Single-Cell RNA Data

Transcriptomics

single-cell

Mehmet Tekman, Bérénice Batut, Anika Erxleben, Wolfgang Maier

Creating, Editing and Importing Galaxy Workflows

Using Galaxy and Managing your Data

workflows

Marius van den Beek

Automating Galaxy workflows using the command line

Using Galaxy and Managing your Data

workflows variant-analysis covid19

Simon Bray, Wolfgang Maier

From peaks to genes

Introduction to Galaxy Analyses

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

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

DIA Analysis using OpenSwathWorkflow

Proteomics

DIA

Matthias Fahrner, Melanie Föll

Machine Learning Modeling of Anticancer Peptides

Proteomics

ML cancer

Jayadev Joshi, Daniel Blankenberg

Mass spectrometry: LC-MS data processing

Metabolomics

Mélanie Petera, Workflow4Metabolomics core team

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

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

RNA-Seq analysis with AskOmics Interactive Tool

Transcriptomics

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

Regression in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

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

Transcriptomics

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

Library Generation for DIA Analysis

Proteomics

DIA

Matthias Fahrner, Melanie Föll

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

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

NGS data logistics

Introduction to Galaxy Analyses

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

Downstream Single-cell RNA analysis with RaceID

Transcriptomics

single-cell

Mehmet Tekman, Alex Ostrovsky

GO Enrichment Analysis

Transcriptomics

IGC Bioinformatics Unit, Maria Doyle

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Epigenetics

Joachim Wolff, Fidel Ramirez, Vivek Bhardwaj, Ekaterina Polkh

How I learned to stop worrying and love the systemd

Galaxy Server administration

ansible systemd

Formation of the Super-Structures on the Inactive X

Epigenetics

ChIP-seq

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

Mapping Jobs to Destinations

Galaxy Server administration

ansible jobs git-gat

Nate Coraor, Björn Grüning, Helena Rasche

Age prediction using machine learning

Statistics and machine learning

Ekaterina Polkh, Anup Kumar

Operating system compatibility

FAQ

Helena Rasche

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Climate

pangeo

Anne Fouilloux

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

Transcriptomics

Florian Heyl, Daniel Maticzka, Bérénice Batut

Exome sequencing data analysis for diagnosing a genetic disease

Variant Analysis

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

Inferring Trajectories using Python (Jupyter Notebook) in Galaxy

Transcriptomics

single-cell 10x paper-replication interactive-tools

Deploying a compute cluster in OpenStack via Terraform

Galaxy Server administration

terraform deploying cloud

Helena Rasche

Galaxy Admin Training Path

FAQ

Helena Rasche

3: RNA-seq genes to pathways

Transcriptomics

mouse

Maria Doyle, Belinda Phipson

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Proteomics

DDA SILAC

Florian Christoph Sigloch, Björn Grüning, Matthias Fahrner

Machine learning: classification and regression

Statistics and machine learning

Anup Kumar, Bérénice Batut

Biomarker candidate identification

Proteomics

DDA human

Florence Combes, David Christiany, Valentin Loux, Yves Vandenbrouck

ToolFactory: Generating Tools From Simple Scripts

Development in Galaxy

Ross Lazarus, Helena Rasche

Peptide and Protein ID using OpenMS tools

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

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

Statistics and machine learning

Kaivan Kamali

Introduction to Machine Learning using R

Statistics and machine learning

interactive-tools

Fotis E. Psomopoulos, Erasmus+ Programme

Galaxy Interactive Tools

Development in Galaxy

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

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

Computational chemistry

Aurélien F. A. Moumbock, Simon Bray

Peptide Library Data Analysis

Proteomics

Jayadev Joshi, Daniel Blankenberg

ATAC-Seq data analysis

Epigenetics

Lucille Delisle, Maria Doyle, Florian Heyl

Training Infrastructure as a Service (TIaaS)

Galaxy Server administration

ansible training jobs git-gat

Helena Rasche, Saskia Hiltemann

Galaxy Tool Management with Ephemeris

Galaxy Server administration

tools git-gat

Martin Čech, Helena Rasche, Nicola Soranzo

Mapping and molecular identification of phenotype-causing mutations

Variant Analysis

Wolfgang Maier

Data Libraries

Galaxy Server administration

ansible storage git-gat

Helena Rasche, Saskia Hiltemann

Identifying tuberculosis transmission links: from SNPs to transmission clusters

Evolution

work-in-progress

Galo A. Goig, Daniela Brites, Christoph Stritt

Whole transcriptome analysis of Arabidopsis thaliana

Transcriptomics

miRNA plants

Cristóbal Gallardo, Pavankumar Videm, Beatriz Serrano-Solano

Bulk RNA Deconvolution with MuSiC

Transcriptomics

single-cell mouse human deconvolution bulk

Mehmet Tekman, Wendi Bacon

EncyclopeDIA

Proteomics

DIA

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

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

Metagenomics

nanopore beer citizen science metagenomics

Text-mining with the SimText toolset

Statistics and machine learning

interactive-tools

Marie Gramm, Dennis Lal group, Daniel Blankenberg

MaxQuant and MSstats for the analysis of label-free data

Proteomics

label-free

Melanie Föll, Matthias Fahrner

16S Microbial analysis with Nanopore data

Metagenomics

nanopore

Cristóbal Gallardo

Creating Galaxy tools from Conda Through Deployment

Development in Galaxy

Alex Ostrovsky, Dave B., Matthias Bernt

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Variant Analysis

cancer cyoa

Jasper Ouwerkerk, Wolfgang Maier, Helena Rasche, Saskia Hiltemann

ToolFactory: Generating Tools From More Complex Scripts

Development in Galaxy

Ross Lazarus

Proteogenomics 2: Database Search

Proteomics

proteogenomics

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

Visualization of RNA-Seq results with CummeRbund

Transcriptomics

Andrea Bagnacani

RStudio in Galaxy

Using Galaxy and Managing your Data

interactive-tools

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

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

Network analysis with Heinz

Transcriptomics

metatranscriptomics network analysis

Chao (Cico) Zhang

Species distribution modeling

Ecology

interactive-tools modeling gbif species populations EBV class

Elisa Michon, Yvan Le Bras, Bérénice Batut

Galaxy 101 for everyone

Introduction to Galaxy Analyses

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

Mass spectrometry imaging: Loading and exploring MSI data

Proteomics

mouse imaging

Melanie Föll, Björn Grüning

Multisample Analysis

Using Galaxy and Managing your Data

collections

Anton Nekrutenko, Anne Pajon

Metaproteomics tutorial

Proteomics

microbiome

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

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

RNA-RNA interactome data analysis

Transcriptomics

Pavankumar Videm

Contributing to BioBlend as a developer

Development in Galaxy

Erik Schill, Simon Bray

metaQuantome 1: Data creation

Proteomics

microbiome

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

Analysis of plant scRNA-Seq Data with Scanpy

Transcriptomics

single-cell plants paper-replication

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

M. tuberculosis Variant Analysis

Variant Analysis

prokaryote

Peter van Heusden, Simon Gladman, Thoba Lose

Differential abundance testing of small RNAs

Transcriptomics

Mallory Freeberg

Pre-processing of 10X Single-Cell RNA Datasets

Transcriptomics

single-cell 10x

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

Clustering in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar

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

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

Mass spectrometry : GC-MS analysis with metaMS package

Metabolomics

work-in-progress

Julien Saint-Vanne

Using dataset collections

Using Galaxy and Managing your Data

collections

Anton Nekrutenko

Data Manipulation Olympics

Introduction to Galaxy Analyses

cyoa

CRISPR screen analysis

Genome Annotation

genome editing CRISPR essential genes cell line

Maria Doyle, Kenji Fujihara, Twishi Gulati

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

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

Essential genes detection with Transposon insertion sequencing

Genome Annotation

bacteria tnseq essential genes

Delphine Lariviere, Bérénice Batut

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

Mass spectrometry: LC-MS preprocessing with XCMS

Metabolomics

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

Mass spectrometry: LC-MS analysis

Metabolomics

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