User: Mads Lerdrup

gravatar for Mads Lerdrup
Mads Lerdrup450
Reputation:
450
Status:
Trusted
Location:
Denmark / Copenhagen / BRIC
Website:
http://easeq.net/
Twitter:
MadsLerdrup
Last seen:
3 years, 8 months ago
Joined:
4 years, 7 months ago
Email:
m***********@bric.ku.dk

Old school biologist. After realizing that I did not do well in rubber boots, I spent a lot of time in the lab and by the confocal doing live cell imaging, but I always lived for the subsequent data analysis.

When I graduated data were sparse and each data point required an effort. With the data-abundance now, the challenge is to focus on the relevant questions and make the investigation and comprehension of the data as intuitive and effortless as possible.

Since I joined BRIC, I have been analyzing the group’s ChIP-seq (and other seq data). I have always been puzzled why seq data requires biologists to write and understand scripting, when other complex data such as high dimensional microscopy, flow cytometry, and high content screening do not.

I kept waiting for someone to make a more intuitive, interactive and visual solution for this, and eventually made my own. The result is called EaSeq and was published recently – you can take a look here: http://easeq.net/ , here: http://dx.doi.org/10.1038/nsmb.3180 and here: https://youtu.be/4_DhQ24qWlk

I’d of course claim that EaSeq will enable a larger group of people to investigate and make use of ChIP-seq data, and even that seasoned people can speed up some processes too, but I trust your judgement more than mine on this :-)

Posts by Mads Lerdrup

<prev • 31 results • page 2 of 4 • next >
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... Thank you for the update and for including EaSeq in you comparison. I think that the forum users who are not that comfortable with command lines will appreciate to learn that adequate GUI-based alternatives do exist. I am also very happy to hear that you appreciate the program - especially in the l ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... As promised, I made some pages explaining the distinction, data requirements, and import further. The entry page is [here][1]. No images yet - Working on that. Please let me know if any of you (also more experienced bioinformaticians) think that there are things that needs to be clarified or changed ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... Thanks for the file. As I mailed you, then the peaks are imported without any problems on my machine. However, only if I import them as Regionsets, which in EaSeq as the genomic locations that you would like to investigate / visualize. EaSeq requires you to import e.g. peaks, enhancers, or CpG-isl ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... Bed files from MACS are usually imported without problems. Could you please mail one of the files that cause troubles to mads.lerdrup@bric.ku.dk ? Then I'll find out why you get this error and how to avoid it. ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data vi
... Good point. Videos should not be at the expense of written tutorials. This is not my home ground, so I have a lot to learn. ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data vi
... That is great, then :-) You are right in that many abstract and reduced presentations become too simplistic - and it might also be hard to assess their robustness. I have always been troubled the focus (of PIs in particular) on the absolute number of peaks as a measure of anything. ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data vi
... Cheers. That is something I should have done from the beginning. I'll do that. ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data vi
... That is correct. If you speak R or Linux fluently, then the (gain)/(time to learn) is of course more modest and depend on type of work and extent. Sasoned bioinformaticians might however be interested in telling their local wet-lab scientists about EaSeq, so that they can do data visualization / a ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data vi
... I agree that playing OS-setup is a rather boring game. I'll prioritize finding out how feasible a cross-platform version is to make - and more importantly how robust it will be... ...
written 4.4 years ago by Mads Lerdrup450
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Comment: C: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data vi
... Thanks for the encouraging view point. Time will tell. I think a cross-platform solution would be preferable and will pursue that if feasible. > Only problem @Mads may face is to find additional people to contribute and keep the project vibrant. Yes. That is true. I have some plans and work th ...
written 4.4 years ago by Mads Lerdrup450

Latest awards to Mads Lerdrup

Popular Question 3.9 years ago, created a question with more than 1,000 views. For EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
Scholar 4.2 years ago, created an answer that has been accepted. For A: Motif not found for protein used for IP?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: How quantitative is Chip-seq?
Good Answer 4.4 years ago, created an answer that was upvoted at least 5 times. For A: How quantitative is Chip-seq?
Commentator 4.4 years ago, created a comment with at least 3 up-votes. For C: How quantitative is Chip-seq?
Supporter 4.4 years ago, voted at least 25 times.
Appreciated 4.5 years ago, created a post with more than 5 votes. For EaSeq - Interactive ChIP-seq analysis and visualization
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: How quantitative is Chip-seq?
Autobiographer 4.5 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 4.5 years ago, created an answer that has been accepted. For A: Motif not found for protein used for IP?
Appreciated 4.6 years ago, created a post with more than 5 votes. For EaSeq - Interactive ChIP-seq analysis and visualization

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