Congratulations to our users!

19. May 2017

What an excellent week for some of our users (and thereby for EaSeq too): Three new stories using EaSeq came out.

Congratulations to these users and their colleagues!

In case that some of you seek inspiration on how to use EaSeq, then take a glance below and in the list of papers made using EaSeq:

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization

Nora EP, Goloborodko A, Valton A-L, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG Cell. ... Read More

Happy Birthday, EaSeq

1. March 2017

Today EaSeq turned one year old, counting from the day our paper went AOP.

I have looked a bit into the statistics to get an impression of how many people (or more correctly: computers) that have been using EaSeq during the last year.

There is a lot that I cannot infer from the available data. But it is clear, that apart from me, then there is a substantial number of people who have been installing EaSeq (>2,500 installations on >1,000 different PCs), a ... Read More

v1.04: PDF export and other plot improvements

27. January 2017

v. 1.04 is out, and while it might not be obvious at first glance, much was changed under EaSeq’s hood when going from version 1.03 to 1.04.

The three most important improvements are:

1) Export plots as pdfs.

I had to make a substantial redesign of the algorithms underlying the plotting part to allow support for pdf output.

The new version has been throughoutly tested and debugged for a couple of months, and to my knowledge, the plots perform ... Read More

New features for beta testing

8. July 2016

The most recent version of EaSeq (v. 1.03) got a new ‘Beta-panel’ (download here).

It can be found in the right side of the Labdesk, below the button for the Navigation panel, and so far it contains a couple of new tools:

The ‘Get Sequences’-tool.

This tool downloads genome sequences (requires some GBs of disk space) from UCSC and export the sequences from a regionset. This is useful if you would like to generate input data for motif finding at a set of peaks ... Read More

ChIP-seq data analysis workshop on April 12

1. April 2016

Would you like to learn how to analyze, explore, and visualize your own and published genome-wide ChIP-seq data?

Then you might be interested in the upcoming workshop ‘ChIP-seq data analysis and visualization for life scientists’, introducing the software environment EaSeq (http://easeq.net/).

EaSeq was recently published and is free of costs, runs on a typical PC, and enables analysis through a graphical user interface. So no need for programming skills or expensive equipment – only basic biological and genomic understanding.

It combines the interactive locus-based exploration ... Read More

New tutorial videos

23. March 2016
I have just uploaded two new video tutorials. Hopefully, I will get time to add more in the coming weeks. So if you have some topics that you would like to learn more about, then please let me know. ... Read More

Sessions files for our paper are available now

3. March 2016
Some of you might be interested in some EaSeq session files to play around with and test its functions. We also thought that it would be good if raw and intermediate EaSeq data from the paper are available for critical inspection. The session files can be found here. ... Read More

EaSeq manuscript published

29. February 2016
It is with great pleasure that we can announce, that the manuscript introducing EaSeq is available as advance online publication in Nature Structural & Molecular Biology. This also means that EaSeq hereby is officially released! We would like to express our gratitude towards everyone who have inspired and contributed in large or small ways. We really appreciate your help and input! ... Read More

Wanted

9. February 2016
I would like to add a future section on this site, with movies that show how to make a particular figure of ChIP-seq analysis using EaSeq. Therefore, if you know a published figure that you would like to learn to make in EaSeq, then please mail it. ... Read More

Running EaSeq on a Mac or Linux machine

24. November 2015
We have now accumulated more experience in running EaSeq on both Mac OS and Linux machines, and it appears to behave exactly as it should. You will need to first install a virtual machine on your machine, and then install Windows on the virtual machine. More information on virtual machines and hardware requirements can be found on the download page and in the FAQ. ... Read More

Poster

19. November 2015
Thanks to the organisers for an excellent conference on Chromatin and Epigenetics with lots of inspiring and illuminating talks. I am grateful for the valuable comments and suggestions on EaSeq that I got. Some of you asked for my poster to be available online. It can be found here. Best wishes, Mads ... Read More

A paper worth of figures in 30 minutes?

7. October 2015

It might be bold to state that EaSeq can accellerate the process of turning comprehensive ChIP-seq datasets into interpretations and figures.

We therefore put this statement to test by remaking the 34 figures and ChIP-seq analyses from Barski et al. (Cell, 129(4):823-37).

Altogether, this took half an hour(*) just by pointing and clicking (see output here), and we believe that this pace is indeed a welcome improvement in analysis time. Especially considering that no programming was involved.

 

(*) Admitted: We did pause between each figure, planned ahead, and the ... Read More

v. 0.97 is out

30. September 2015

We are happy to release v. 0.97. The user experience has been improved markedly, so we recommend upgrading older versions of EaSeq to v. 0.97.

Among other things, the GUI controlling the plot handling has been completely remade from scratch, and now runs more efficiently and smoothly. It has been tested in a range of conditions for a while, but there might still be a bug or two hiding. So please let us know if it misbehaves in your hands.

The Tutorials were affected by this ... Read More

What is cooking?

16. September 2015
A manuscript introducing EaSeq was submitted to a journal in June. We have therefore focused on improving EaSeq according to the feedback we got from the reviewers of the manuscript. A new release (v 0.97) that integrates most of this (and a lot of bug-fixes) will be available soon, and we plan on resubmitting the manuscript in October. ... Read More

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