User: Endre Bakken Stovner

Reputation:
880
Status:
Trusted
Location:
Norway
Website:
https://github.com/end...
Last seen:
3 years, 5 months ago
Joined:
5 years ago
Email:
e*******@idi.ntnu.no

PhD student and bioinformatician. Uni homepage: http://www.ntnu.edu/employees/endrebak

Posts by Endre Bakken Stovner

<prev • 137 results • page 1 of 14 • next >
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Comment: C: Metrics for exploring the parameter space of broad domain chip-seq finders?
... I already starred your repo. Since I use Python, I might go with meta-seq, but great job all the same! ...
written 3.5 years ago by Endre Bakken Stovner880
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Metrics for exploring the parameter space of broad domain chip-seq finders?
... Let us say I have want to use SICER or MACS2 for finding broad domains in ChIP-seq data. These contain plenty of parameters I can tune to change the domains found. Are there any metrics I can use to see if some parameters perform better than others? Any idea, no matter how seemingly stupid, would b ...
chip-seq written 3.5 years ago by Endre Bakken Stovner880 • updated 3.5 years ago by dariober10k
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QC for broad domain chip-seq data?
... If you do narrow peak calling you can do autocorrelation as a form of QC. This is just comparing the peaks from the two-strands for the same potential peak. I cannot think of anything similar that would work on broad domains. Some stupid ideas for QC to get the creative juices flowing: Find reg ...
chip-seq written 3.5 years ago by Endre Bakken Stovner880 • updated 3.4 years ago by Biostar ♦♦ 20
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Comment: C: Bug in bx-python maf?
... Do not remember anything about this stuff, sorry! ...
written 3.5 years ago by Endre Bakken Stovner880
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Comment: C: KEGG pathway per genes relation
... Can you show some example input and desired output? ...
written 3.7 years ago by Endre Bakken Stovner880
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Comment: C: Advice for undergraduate bioinformatics learners
... Agreed, take an intro course to molecular biology and learn the fundamentals of genetics. ...
written 3.7 years ago by Endre Bakken Stovner880
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Comment: C: problem with KEGG pathway gene extraction
... That is something on your end. The CLI and API uses the same code. It probably stems from you having multiple versions of Python installed and different versions of the library installed for each. If you encounter more problems please tell me at https://github.com/endrebak/kg/issues   ...
written 3.8 years ago by Endre Bakken Stovner880
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Comment: C: problem with KEGG pathway gene extraction
... Now it should work. pip install kg==0.0.8 ...
written 3.8 years ago by Endre Bakken Stovner880
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Comment: C: problem with KEGG pathway gene extraction
... I'll fix it later today, thanks. ...
written 3.8 years ago by Endre Bakken Stovner880
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Comment: C: problem with KEGG pathway gene extraction
... I have updated kg and added an example of how to use it from within python: https://github.com/endrebak/kg pip install kg==0.0.7  ...
written 3.8 years ago by Endre Bakken Stovner880

Latest awards to Endre Bakken Stovner

Student 3.8 years ago, asked a question with at least 3 up-votes. For Publishing improved versions of algorithms - ethics and norms.
Voter 3.9 years ago, voted more than 100 times.
Centurion 3.9 years ago, created 100 posts.
Scholar 4.0 years ago, created an answer that has been accepted. For A: Mapping refseq transcripts to encoded proteins (NM_ to NP_)
Scholar 4.0 years ago, created an answer that has been accepted. For A: Mapping refseq transcripts to encoded proteins (NM_ to NP_)
Appreciated 4.0 years ago, created a post with more than 5 votes. For New Python/R interface in pre-alpha: wide diapeR
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Asking for opinions about Bioinformatics Data Skills book
Scholar 4.1 years ago, created an answer that has been accepted. For A: Mapping refseq transcripts to encoded proteins (NM_ to NP_)
Appreciated 4.1 years ago, created a post with more than 5 votes. For New Python/R interface in pre-alpha: wide diapeR
Supporter 4.4 years ago, voted at least 25 times.
Student 4.4 years ago, asked a question with at least 3 up-votes. For Publishing improved versions of algorithms - ethics and norms.
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Get gene names from rs SNP ids
Scholar 4.7 years ago, created an answer that has been accepted. For A: Mapping refseq transcripts to encoded proteins (NM_ to NP_)
Scholar 4.8 years ago, created an answer that has been accepted. For A: Mapping refseq transcripts to encoded proteins (NM_ to NP_)
Autobiographer 5.0 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 5.0 years ago, created an answer that has been accepted. For A: Mapping refseq transcripts to encoded proteins (NM_ to NP_)

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