Admin: Istvan Albert
Istvan Albert ♦♦ 81k
- Reputation:
- 81,040
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 47 minutes ago
- Joined:
- 10 years ago
- Email:
- i************@gmail.com
I have published research works in the fields of granular matter physics, network science, machine learning, user interfaces and bioinformatics. But above all I like to create useful systems. I enjoy the process of designing and implementing web based services that stand the test of time. My current project that I dedicate most my time to is an e-book on genomic data analysis:
- The Biostar Handbook - it is modeled by the content on this site and is a comprehensive guide for beginning bioinformaticians.
I am the maintainer of this site:
- Biostar Q&A platform more of a jack-of-all-trades: lead developer, interface designer, database manager, sys admin, dev-ops etc. whatever needs to be done.
Currently I work as a Professor of Bioinformatics at Penn State. Within that position I serve in various roles:
- Director of the Bioinformatics Consulting Center at Penn State
- Bioinformatics instructor
- Researcher and tool developer GeneTrack, and a few others
Posts by Istvan Albert
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... The way to do it is to go to your user account and change your email.
In addition, you may click on the **about** link and will show the `admin@biostars.org` email for contact.
...
written 26 days ago by
Istvan Albert ♦♦ 81k
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Answer:
A: Multiple alignment software
... An important detail that should be mentioned here is that none of the alignments you present there are inherently "good" or "bad"
Alignment algorithms maximize a score. The result (if implemented correctly) is the alignment that produces the maximal score. The score is built from the rewards and pe ...
written 4 weeks ago by
Istvan Albert ♦♦ 81k
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... The better tool to verify patterns that will include overlapping matches is the [dreg][dreg] tool from emboss
cat NC_001798.fa | dreg -filter -pattern GGGCGGGGGTCGGGCGGGCGGGGGTCGGGCG
[dreg]: http://emboss.sourceforge.net/apps/cvs/emboss/apps/dreg.html
produces 13 matches
#=============== ...
written 5 weeks ago by
Istvan Albert ♦♦ 81k
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... They (the Avi Mayan' lab) have also built Enrichr, Clustergrammer, and other tools:
http://amp.pharm.mssm.edu/Enrichr/
https://clustergrammer.readthedocs.io/getting_started.html
...
written 5 weeks ago by
Istvan Albert ♦♦ 81k
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... The clusterprofiler seems like a quite sophisticated tool - a bit overcomplicated in that it is not clear what data goes into it, so one has devote quite the effort to get their data in the right shape and form - but after that looks like it does quite a bit
https://github.com/YuLab-SMU/clusterProf ...
written 5 weeks ago by
Istvan Albert ♦♦ 81k
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... I am trying to catch up with the latest development in the gene set enrichment analysis and I am looking for recommendations describing practices and approaches that I might have missed. Perhaps older methods are still the best.
Here is the question:
Suppose you ran an analysis pipeline that produ ...
written 5 weeks ago by
Istvan Albert ♦♦ 81k
1
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... I want to mention here that conda activation works differently starting with conda 4.6
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
they have removed the `source activate` approach and replaced it with `conda activate`
For the original poster I would r ...
written 7 weeks ago by
Istvan Albert ♦♦ 81k
1
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Answer:
A: Create a gold standard
... Here is a relevant publication: [Is it time to change the reference genome][1]?
In a nutshell, my takeaway is that "gold standard" is not the right nomenclature. We should be thinking about a consensus sequence where every base is a major allele.
* https://genomebiology.biomedcentral.com/articles ...
written 8 weeks ago by
Istvan Albert ♦♦ 81k
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... Hello https://www.biostars.org/u/11714/ - your suggestion to list additional learning resources after each chapter is excellent.
We will add that over the next semester.
On new chapters, it is a bit of a challenge to figure out what to cover next. PacBio, single-cell RNA-Seq and metagenomics are a ...
written 9 weeks ago by
Istvan Albert ♦♦ 81k
1
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... Thanks for the feedback.
For what is worth, I think that BASH prompt is best that I found - though I may have not properly explained why you'd want that information. I will be updating that section to include the following:
The bash prompt should give you information on the context that you are w ...
written 11 weeks ago by
Istvan Albert ♦♦ 81k
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