Orange Blog

Author: Ajda Pretnar, Jun 3, 2019

Gene Expression Profiles with Line Plot

Line Plot is one of our recent additions to the visualization widgets. It shows data profiles, meaning it plots values for all features in the data set. Each data instance in a line plot is a line or a ‘profile’. The widget can show four types of information – individual data profiles (lines), data range, mean profile and error bars. It has the same cool features of other Orange visualizations – it is interactive, meaning you can select a subset of data instances from the plot, it allows grouping by a discrete variable, and it highlights an incoming data subset.


Author: 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.


Author: 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.


Author: 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.


Author: 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.


Author: 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.


Author: 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.


Author: 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.


Author: AJDA, Jun 5, 2015

Data Fusion Add-on for Orange

Orange is about to get even more exciting! We have created a prototype add-on for data fusion, which will certainly be of interest to many users. Data fusion brings large heterogeneous data sets together to create sensible clusters of related data instances and provides a platform for predictive modelling and recommendation systems. This widget set can be used either to recommend you the next movie to watch based on your demographic characteristics, movies you gave high scores to, your preferred genre, etc.


Author: BLAZ, Oct 24, 2014

Hands-on Orange at Functional Genomics Workshop

Last week we have co-organized a Functional Genomics Workshop. At University of Ljubljana we have hosted an inspiring pack of scientists from the Donnelly Centre for Cellular and Biomolecular Research from Toronto. Part of the event was a hands-on workshop Data mining without programing, where we have used Orange to analyze data from systems biology. Data included a subset of Charlie Boone’s famous yeast interaction data and data from chemical genomics.

Categories: bioinformatics