Search Tutorials

Pangeo Notebook in Galaxy - Introduction to Xarray

Climate

pangeo interactive-tools jupyter-notebook jupyter-notebook

Anne Fouilloux

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Climate

pangeo

Anne Fouilloux

Visualization of Climate Data using NetCDF xarray Map Plotting

Ecology

pangeo

Soumya Jha

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

Pre-processing of 10X Single-Cell RNA Datasets

Transcriptomics

single-cell 10x

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

Galaxy 101 for everyone

Introduction to Galaxy Analyses

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

From peaks to genes

Introduction to Galaxy Analyses

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

High Throughput Molecular Dynamics and Analysis

Computational chemistry

Simon Bray, Tharindu Senapathi, Christopher Barnett, Björn Grüning

Automating Galaxy workflows using the command line

Using Galaxy and Managing your Data

workflows variant-analysis covid19

Simon Bray, Wolfgang Maier

Visualize Climate data with Panoply netCDF viewer

Climate

interactive-tools

Anne Fouilloux

Genome assembly using PacBio data

Assembly

assembly pacbio

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

Understanding Galaxy history system

Using Galaxy and Managing your Data

Anton Nekrutenko, Martin Čech, Helena Rasche

Visualization of RNA-Seq results with Volcano Plot in R

Transcriptomics

interactive-tools

Maria Doyle

Visualize EBV cube data with Panoply netCDF viewer

Ecology

interactive-tools EBV cube Data visualization

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

MaxQuant and MSstats for the analysis of TMT data

Proteomics

DDA TMT

Klemens Fröhlich, Melanie Föll, Matthias Fahrner

Extracting Workflows from Histories

Using Galaxy and Managing your Data

workflows

Dave Clements

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

Proteomics

Florian Christoph Sigloch, Björn Grüning

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

Climate

interactive-tools

Anne Fouilloux

Creating Galaxy tools from Conda Through Deployment

Development in Galaxy

Alex Ostrovsky, Dave B., Matthias Bernt

CRISPR screen analysis

Genome Annotation

genome editing CRISPR essential genes cell line

Maria Doyle, Kenji Fujihara, Twishi Gulati

Chloroplast genome assembly

Assembly

plants nanopore

Anna Syme

Somatic Variant Discovery from WES Data Using Control-FREEC

Variant Analysis

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

Tree thinking for tuberculosis evolution and epidemiology

Evolution

prokaryotes phylogenetics evolution work-in-progress

Christoph Stritt, Daniela Brites, Galo A. Goig

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Variant Analysis

cancer cyoa

Jasper Ouwerkerk, Wolfgang Maier, Helena Rasche, Saskia Hiltemann

Unicycler Assembly

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Simon Gladman

Genome Assembly of MRSA using Illumina MiSeq Data

Assembly

illumina assembly amr

Genome annotation with Funannotate

Genome Annotation

eukaryote

How I learned to stop worrying and love the systemd

Galaxy Server administration

ansible systemd

Analysis of plant scRNA-Seq Data with Scanpy

Transcriptomics

single-cell plants paper-replication

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

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

Computational chemistry

Aurélien F. A. Moumbock, Simon Bray

VGP assembly pipeline

Assembly

pacbio eukaryote VGP

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

How to reproduce published Galaxy analyses

Introduction to Galaxy Analyses

Melanie Föll, Anne Fouilloux

ToolFactory: Generating Tools From More Complex Scripts

Development in Galaxy

Ross Lazarus

Getting your hands-on climate data

Climate

Anne Fouilloux

NGS data logistics

Introduction to Galaxy Analyses

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

IGV Introduction

Introduction to Galaxy Analyses

Anton Nekrutenko, Joachim Wolff, Anne Pajon

Inferring Trajectories using Python (Jupyter Notebook) in Galaxy

Transcriptomics

single-cell 10x paper-replication interactive-tools

Upgrading Galaxy

Galaxy Server administration

ansible

Simon Gladman

Mass spectrometry imaging: Finding differential analytes

Metabolomics

Melanie Föll

Antibiotic resistance detection

Metagenomics

nanopore plasmids assembly amr

Willem de Koning, Saskia Hiltemann

RStudio in Galaxy

Using Galaxy and Managing your Data

interactive-tools

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

Where can I get planemo?

FAQ

Alex Ostrovsky, Dave B., Matthias Bernt

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

Variant Analysis

Wolfgang Maier

A short introduction to Galaxy

Introduction to Galaxy Analyses

español

Anna Syme, Nicola Soranzo

Machine learning: classification and regression

Statistics and machine learning

Anup Kumar, Bérénice Batut

Genome Assembly of MRSA using Oxford Nanopore MinION Data

Assembly

nanopore assembly amr

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

Differential abundance testing of small RNAs

Transcriptomics

Mallory Freeberg

Introduction to Genomics and Galaxy

Introduction to Galaxy Analyses

Dave Clements, Cristóbal Gallardo

VGP assembly pipeline - short version

Assembly

pacbio eukaryote VGP

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

Galaxy Interactive Tools

Development in Galaxy

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

Multisample Analysis

Using Galaxy and Managing your Data

collections

Anton Nekrutenko, Anne Pajon

Automation with Jenkins

Galaxy Server administration

ansible automation

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

De novo transcriptome assembly, annotation, and differential expression analysis

Transcriptomics

work-in-progress

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

Connecting Galaxy to a compute cluster

Galaxy Server administration

jobs ansible git-gat

Nate Coraor, Björn Grüning, Helena Rasche

Bulk RNA Deconvolution with MuSiC

Transcriptomics

single-cell mouse human deconvolution bulk

Mehmet Tekman, Wendi Bacon

Analyse HeLa fluorescence siRNA screen

Imaging

Thomas Wollmann

Peptide and Protein ID using SearchGUI and PeptideShaker

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Age prediction using machine learning

Statistics and machine learning

Ekaterina Polkh, Anup Kumar

Pre-processing of Single-Cell RNA Data

Transcriptomics

single-cell

Mehmet Tekman, Bérénice Batut, Anika Erxleben, Wolfgang Maier

Quality Control

Sequence analysis

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

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Climate

interactive-tools

Anne Fouilloux, Hui Tang

Basics of machine learning

Statistics and machine learning

Anup Kumar

Introduction to deep learning

Statistics and machine learning

Anup Kumar, Alireza Khanteymoori

Visualisation with Circos

Visualisation

Saskia Hiltemann, Helena Rasche, Cristóbal Gallardo

Protein-ligand docking

Computational chemistry

Simon Bray

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

FAQ

Peter van Heusden

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

FAQ

Ross Lazarus

Trajectory Analysis using Monocle3

Transcriptomics

single-cell trajectory-analysis paper-replication

Whole transcriptome analysis of Arabidopsis thaliana

Transcriptomics

miRNA plants

Cristóbal Gallardo, Pavankumar Videm, Beatriz Serrano-Solano

Galaxy 101

Introduction to Galaxy Analyses

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

Making sense of a newly assembled genome

Assembly

prokaryote

Anton Nekrutenko, Delphine Lariviere, Helena Rasche

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

Variant Analysis

covid19

Wolfgang Maier, Bérénice Batut

3: RNA-seq genes to pathways

Transcriptomics

mouse

Maria Doyle, Belinda Phipson

Identifying tuberculosis transmission links: from SNPs to transmission clusters

Evolution

work-in-progress

Galo A. Goig, Daniela Brites, Christoph Stritt

Label-free data analysis using MaxQuant

Proteomics

DDA label-free

Melanie Föll, Matthias Fahrner

External Authentication

Galaxy Server administration

authentication

Nate Coraor, Nicola Soranzo, Helena Rasche

Protein FASTA Database Handling

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

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

Statistics and machine learning

Kaivan Kamali

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

Transcriptomics

Florian Heyl, Daniel Maticzka, Bérénice Batut

Reference-based RNAseq data analysis (long)

Transcriptomics

work-in-progress

Anton Nekrutenko

Proteogenomics 3: Novel peptide analysis

Proteomics

proteogenomics

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

M. tuberculosis Variant Analysis

Variant Analysis

prokaryote

Peter van Heusden, Simon Gladman, Thoba Lose

Mass spectrometry imaging: Examining the spatial distribution of analytes

Metabolomics

Melanie Föll, Maren Stillger

1: RNA-Seq reads to counts

Transcriptomics

collections mouse QC

Maria Doyle, Belinda Phipson, Harriet Dashnow

RNA-Seq analysis with AskOmics Interactive Tool

Transcriptomics

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

Library Generation for DIA Analysis

Proteomics

DIA

Matthias Fahrner, Melanie Föll

Submitting sequence data to ENA

Using Galaxy and Managing your Data

covid19

Miguel Roncoroni, Bert Droesbeke

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

FAQ

Ross Lazarus

De novo transcriptome reconstruction with RNA-Seq

Transcriptomics

Mallory Freeberg, Mo Heydarian

Introduction to image analysis using Galaxy

Imaging

Thomas Wollmann, Saskia Hiltemann

DIA Analysis using OpenSwathWorkflow

Proteomics

DIA

Matthias Fahrner, Melanie Föll

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

RAD-Seq Reference-based data analysis

Ecology

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

Yvan Le Bras

Infinium Human Methylation BeadChip

Epigenetics

Katarzyna Murat, Krzysztof Poterlowicz

Using dataset collections

Using Galaxy and Managing your Data

collections

Anton Nekrutenko

JupyterLab in Galaxy

Using Galaxy and Managing your Data

interactive-tools

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

Metagenomics

nanopore beer citizen science metagenomics

Regression in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

RNA-RNA interactome data analysis

Transcriptomics

Pavankumar Videm

De Bruijn Graph Assembly

Assembly

Simon Gladman, Helena Rasche, Saskia Hiltemann

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

Transcriptomics

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

Peptide and Protein ID using OpenMS tools

Proteomics

DDA

Florian Christoph Sigloch, Björn Grüning

Mass spectrometry imaging: Loading and exploring MSI data

Proteomics

mouse imaging

Melanie Föll, Björn Grüning

Classification in Machine Learning

Statistics and machine learning

Alireza Khanteymoori, Anup Kumar, Simon Bray

Mass spectrometry: LC-MS data processing

Metabolomics

Mélanie Petera, Workflow4Metabolomics core team

FASTQ format

FAQ

Bérénice Batut

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Epigenetics

Joachim Wolff, Fidel Ramirez, Vivek Bhardwaj, Ekaterina Polkh

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

Assembly

covid19

Wolfgang Maier

ToolFactory: Generating Tools From Simple Scripts

Development in Galaxy

Ross Lazarus, Helena Rasche

JavaScript plugins

Development in Galaxy

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

EncyclopeDIA

Proteomics

DIA

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

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

Galaxy Interactive Tools

Galaxy Server administration

ansible interactive-tools

Nate Coraor, Simon Gladman, Helena Rasche, Anthony Bretaudeau

Introduction to Machine Learning using R

Statistics and machine learning

interactive-tools

Fotis E. Psomopoulos, Erasmus+ Programme

Refining Genome Annotations with Apollo (prokaryotes)

Genome Annotation

prokaryote

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

Peptide Library Data Analysis

Proteomics

Jayadev Joshi, Daniel Blankenberg

What should I do special if on usegalaxy.be?

FAQ

Bert Droesbeke

Masking repeats with RepeatMasker

Genome Annotation

eukaryote

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

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

Use Jupyter notebooks in Galaxy

Using Galaxy and Managing your Data

Delphine Lariviere

Which search algorithms are recommended for searching the metaproteomics data?

FAQ

Milla Berezutskaia

Formation of the Super-Structures on the Inactive X

Epigenetics

ChIP-seq

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

Downloading and Deleting Data in Galaxy

Using Galaxy and Managing your Data

Simon Gladman, Helena Rasche

Clustering 3K PBMCs with Scanpy

Transcriptomics

single-cell 10x

Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman

Genome Assembly Quality Control

Assembly

assembly quality control

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

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

FAQ

Peter van Heusden

Image classification in Galaxy with fruit 360 dataset

Statistics and machine learning

Kaivan Kamali

Customising the welcome page

FAQ

Helena Rasche

Mass spectrometry: LC-MS analysis

Metabolomics

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

Workflow Reports

Using Galaxy and Managing your Data

workflows

metaQuantome 1: Data creation

Proteomics

microbiome

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

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

Machine Learning Modeling of Anticancer Peptides

Proteomics

ML cancer

Jayadev Joshi, Daniel Blankenberg

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

Ansible

Galaxy Server administration

ansible

Helena Rasche, Saskia Hiltemann

Comparative gene analysis in unannotated genomes

Genome Annotation

evolution annotation vgp cookbook eukaryote prokaryote

Anton Nekrutenko

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

Proteogenomics 1: Database Creation

Proteomics

proteogenomics

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

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

Using Galaxy and Managing your Data

ncbi covid19

Jon Trow, Adelaide Rhodes

TB Variant Report crashes (with an error about KeyError: 'protein')

FAQ

Peter van Heusden, Helena Rasche

Data Manipulation Olympics

Introduction to Galaxy Analyses

cyoa

Proteogenomics 2: Database Search

Proteomics

proteogenomics

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

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

ATAC-Seq data analysis

Epigenetics

Lucille Delisle, Maria Doyle, Florian Heyl

Essential genes detection with Transposon insertion sequencing

Genome Annotation

bacteria tnseq essential genes

Delphine Lariviere, Bérénice Batut

Single-cell quality control with scater

Transcriptomics

single-cell

Graham Etherington, Nicola Soranzo

Microbial Variant Calling

Variant Analysis

prokaryote

Anna Syme, Simon Gladman, Torsten Seemann

Creating, Editing and Importing Galaxy Workflows

Using Galaxy and Managing your Data

workflows

Marius van den Beek

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Proteomics

DDA SILAC

Florian Christoph Sigloch, Björn Grüning, Matthias Fahrner

Refining Genome Annotations with Apollo (eukaryotes)

Genome Annotation

eukaryote cyoa

Anthony Bretaudeau, Erasmus+ Programme

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

metaQuantome 2: Function

Proteomics

microbiome

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

metaQuantome 3: Taxonomy

Proteomics

microbiome

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

Running molecular dynamics simulations using GROMACS

Computational chemistry

Simon Bray

Galaxy Monitoring with Telegraf and Grafana

Galaxy Server administration

ansible monitoring git-gat

Helena Rasche

An Introduction to Genome Assembly

Assembly

Simon Gladman

Nucleoli segmentation and feature extraction using CellProfiler

Imaging

Beatriz Serrano-Solano, Jean-Karim Hériché

Visualization of RNA-Seq results with heatmap2

Transcriptomics

Maria Doyle

Downstream Single-cell RNA analysis with RaceID

Transcriptomics

single-cell

Mehmet Tekman, Alex Ostrovsky

Calling variants in non-diploid systems

Variant Analysis

prokaryote

Anton Nekrutenko, Alex Ostrovsky

Mapping Jobs to Destinations

Galaxy Server administration

ansible jobs git-gat

Nate Coraor, Björn Grüning, Helena Rasche

Generic plugins

Development in Galaxy

Saskia Hiltemann, Youri Hoogstrate

Visualization of RNA-Seq results with Volcano Plot

Transcriptomics

Maria Doyle

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

FAQ

Wendi Bacon, Mehmet Tekman, Rahmot Afolabi

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

Galaxy Webhooks

Development in Galaxy

Clemens Blank, Martin Čech, Björn Grüning

Mass spectrometry: LC-MS preprocessing with XCMS

Metabolomics

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

Galaxy Monitoring with gxadmin

Galaxy Server administration

monitoring ansible git-gat

Helena Rasche

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

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

FAQ

Rahmot Afolabi

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

Galaxy Database schema

Galaxy Server administration

Hans-Rudolf Hotz, Björn Grüning

From small to large-scale genome comparison

Genome Annotation

Esteban Perez-Wohlfeil

Install tools via the Admin UI

FAQ

Saskia Hiltemann

Species distribution modeling

Ecology

interactive-tools modeling gbif species populations EBV class

Elisa Michon, Yvan Le Bras, Bérénice Batut

Could I use a different p-adj value for filtering differentially expressed genes?

FAQ

Cristóbal Gallardo

RAD-Seq de-novo data analysis

Ecology

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

Yvan Le Bras

Small Non-coding RNA Clustering using BlockClust

Transcriptomics

Pavankumar Videm

InterMine integration with Galaxy

Using Galaxy and Managing your Data

Daniela Butano, Yo Yehudi

Analyses of metagenomics data - The global picture

Metagenomics

Saskia Hiltemann, Bérénice Batut

Galaxy Tool Management with Ephemeris

Galaxy Server administration

tools git-gat

Martin Čech, Helena Rasche, Nicola Soranzo

RNA Seq Counts to Viz in R

Transcriptomics

interactive-tools

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

Visualization of RNA-Seq results with CummeRbund

Transcriptomics

Andrea Bagnacani

Enable upload via FTP

Galaxy Server administration

data git-gat

Lucille Delisle

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

Proteomics

DDA human

Valentin Loux, Florence Combes, David Christiany, Yves Vandenbrouck

Rule Based Uploader: Advanced

Using Galaxy and Managing your Data

collections tags

John Chilton, Helena Rasche

Debugging Galaxy

Development in Galaxy

Assunta DeSanto, John Davis, John Chilton

Contributing to BioBlend as a developer

Development in Galaxy

Erik Schill, Simon Bray

Understanding Barcodes

Transcriptomics

single-cell

Mehmet Tekman

Galaxy Installation with Ansible

Galaxy Server administration

ansible deploying git-gat

Writing Automated Tests for Galaxy

Development in Galaxy

John Davis, John Chilton

Preparing genomic data for phylogeny reconstruction

Ecology

phylogeny data handling functional annotation

Miguel Roncoroni, Brigida Gallone

Combining datasets after pre-processing

Transcriptomics

single-cell 10x paper-replication español

Generating a single cell matrix using Alevin

Transcriptomics

single-cell 10x paper-replication español

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

Statistics and machine learning

Kaivan Kamali

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

Computational chemistry

covid19

Simon Bray

Deploying a compute cluster in OpenStack via Terraform

Galaxy Server administration

terraform deploying cloud

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

16S Microbial analysis with Nanopore data

Metagenomics

nanopore

Cristóbal Gallardo

Calling very rare variants

Variant Analysis

work-in-progress

Anton Nekrutenko, Nick Stoler

Calling variants in diploid systems

Variant Analysis

Anton Nekrutenko, Nicola Soranzo