Statistics and machine learning

Statistical Analyses for omics data and machine learning using Galaxy tools

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour
Age prediction using machine learning
tutorial zenodo_link workflow
Basics of machine learning
tutorial zenodo_link workflow interactive_tour
Classification in Machine Learning
tutorial zenodo_link workflow
Clustering in Machine Learning
tutorial zenodo_link workflow
Deep Learning (Part 1) - Feedforward neural networks (FNN)
slides tutorial zenodo_link workflow
Deep Learning (Part 2) - Recurrent neural networks (RNN)
slides tutorial zenodo_link workflow
Deep Learning (Part 3) - Convolutional neural networks (CNN)
slides tutorial zenodo_link workflow
Interval-Wise Testing for omics data
tutorial zenodo_link workflow interactive_tour
Introduction to deep learning
tutorial zenodo_link workflow
Introduction to Machine Learning using R
level level level
tutorial
Machine learning: classification and regression
tutorial zenodo_link workflow interactive_tour
PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
tutorial zenodo_link workflow
Regression in Machine Learning
tutorial zenodo_link workflow
Text-mining with the SimText toolset
tutorial zenodo_link workflow

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/statistics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Maintainers

This material is maintained by:

Marzia A CremonaMarzia A Cremona Fabio CumboFabio Cumbo Anup KumarAnup Kumar

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Ekaterina PolkhEkaterina Polkh Anup KumarAnup Kumar Alireza KhanteymooriAlireza Khanteymoori Simon BraySimon Bray Kaivan KamaliKaivan Kamali Marzia A CremonaMarzia A Cremona Fabio CumboFabio Cumbo Fotis E. PsomopoulosFotis E. Psomopoulos Bérénice BatutBérénice Batut VijayVijay Daniel BlankenbergDaniel Blankenberg Marie GrammMarie Gramm Dennis Lal groupDennis Lal group