By: Martin Špendl, Feb 23, 2023
Single-sample GSEA is now in Orange
Single-sample extension of Gene Set Enrichment Analysis now in Bioinformatics add-on.
Orange Blog
By: Blaž Zupan, Jul 25, 2019
Orange at ISMB/ECCB 2019
Our entry to this year’s largest bioinformatics conference was on the training of single-cell data analytics. We claim that with Orange and its new single-cell RNA analysis add-on, one can assemble a workshop to teach essential concepts from single-cell analytics in a single day. \ Single-cell genomics is driven on revolutionary technology from molecular biology that allows us to peek into inner workings of the individual cell. Single-cell datasets feature thousands of genes and cells and benefit from the analysis that integrates this data with other knowledge sources, like those on the classification of genes, lists of pathways, and sets of cell-type markers.
By: Ajda Pretnar, Jun 3, 2019
Gene Expression Profiles with Line Plot
Line Plot shows profiles of data instances – each instance is a line in the plot and its profile are values across all variables in the data. We show how to explore gene expression profiles.
By: AJDA, May 30, 2018
Spectroscopy Workshop at BioSpec and How to Merge Data
Last week Marko and I visited the land of the midnight sun - Norway! We held a two-day workshop on spectroscopy data analysis in Orange at the Norwegian University of Life Sciences. The students from BioSpec lab were yet again incredible and we really dug deep into Orange. Related: Orange with Spectroscopy Add-on A class full of dedicated scientists. One thing we did was see how to join data from two different sources.
By: BLAZ, Mar 6, 2017
Orange Workshops: Luxembourg, Pavia, Ljubljana
February was a month of Orange workshops. Ljubljana: Biologists We (Tomaž, Martin and I) have started in Ljubljana with a hands-on course for the COST Action FA1405 Systems Biology Training School. This was a four hour workshop with an introduction to classification and clustering, and then with application of machine learning to analysis of gene expression data on a plant called Arabidopsis. The organization of this course has even inspired us for a creation of a new widget GOMapMan Ontology that was added to Bioinformatics add-on.
By: AJDA, Feb 3, 2017
For When You Want to Transpose a Data Table...
Sometimes, you need something more. Something different. Something, that helps you look at the world from a different perspective. Sometimes, you simply need to transpose your data. Since version 3.3.9, Orange has a Transpose widget that flips your data table around. Columns become rows and rows become columns. This is often useful, if you have, say, biological data. Related: Datasets in Orange Bioinformatics Today we will play around with brown-selected.tab, a data set on gene expression levels for 79 experiments.
By: BLAZ, Oct 2, 2016
Intro to Data Mining for Life Scientists
RNA Club Munich has organized Molecular Life of Stem Cells Conference in Ljubljana this past Thursday, Friday and Saturday. They asked us to organize a four-hour workshop on data mining. And here we were: four of us, Ajda, Anze, Marko and myself (Blaz) run a workshop for 25 students with molecular biology and biochemistry background. We have covered some basic data visualization, modeling (classification) and model scoring, hierarchical clustering and data projection, and finished with a touch of deep-learning by diving into image analysis by deep learning-based embedding.
By: AJDA, Jul 31, 2015
Datasets in Orange Bioinformatics Add-On
As you might know, Orange comes with several basic widget sets pre-installed. These allow you to upload and explore the data, visualize them, learn from them and make predictions. However, there are also some exciting add-ons available for installation. One of these is a bioinformatics add-on, which is our specialty. Bioinformatics widget set allows you to pursue complex analysis of gene expression by providing access to several external libraries. There are four widgets intended specifically for this - dictyExpress, GEO Data Sets, PIPAx and GenExpress.
By: AJDA, Jun 19, 2015
Orange workshops around the world
Even though the summer is nigh, we are hardly going to catch a summer break this year. Orange team is busy holding workshops around the world to present the latest widgets and data mining tools to the public. Last week we had a very successful tutorial at [BC]2 in Basel, Switzerland, where Marinka and Blaž presented data fusion. A part of the tutorial was a hands-on workshop with Orange’s new add-on for data fusion.
By: MARINKAZ, Jun 8, 2015
Data Fusion Tutorial at the [BC]^2
We are excited to host a three-hour tutorial on data fusion at the Basel Computational Biology Conference. To this end we have prepared a series of short lectures notes that accompany the recently developed Data Fusion Add-on for Orange. We design the tutorial for data mining researchers and molecular biologists with interest in large-scale data integration. In the tutorial we focus on collective latent factor models, a popular class of approaches for data fusion.