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Hi, Peptide Shaker is crashing when I ask to use the PEP statistical analysis instead of FDR. I read a useful article on interpreting data and the PEP would be useful for me, since I just want to be s…
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I was curious if you have any specific reason to only implement RDA taxonomy annotation and/but not blast ? People criticize RDA because of its lack of sensitivity.
Thanks.
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**Background**: Protein 3D structures are very useful when studying the effect of mutations in cancer. For example, oftentimes mutations tend to occur in the same 3D space. In the cBioPortal, we map a…
jjgao updated
7 years ago
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As I mentioned, each student will have a "project" that results in a "product". Do you have any preference to what such project is involved with? What is one idea that comes to mind based on the readi…
sr320 updated
8 years ago
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Current docs state:
```
/**
The ID defined by the external onotology source.
(e.g. `http://purl.obolibrary.org/obo/OBI_0001271`)
*/
string id;
```
This is fairly open ended and we can imag…
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Hello there,
This is Olga Botvinnik and Mike Lovci (@mlovci), PhD students in Bioinformatics-type fields at UC-San Diego working on a biological data analysis package for "large" (for biology) dataset…
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```
What steps will reproduce the problem?
1.>>> from pygr import worldbase
2.>>> worldbase.dir()
3.
What is the expected output? What do you see instead?
A list of databases expect but will get this…
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### Introduction
I've always found it's been a real pain for computational biologists to interact with ontologies in Python. The ontology community seems focused on java products and the file formats…
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chromosome organzation is linked through is_a
histone H4-R3 methylation
histone H3-S10 phosphorylation
histone H4-K8 acetylation
which seems incorrrect. The problem may be at
chromatin modification
…
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I joined the Matchmaker Exchange group late last year. After reading up the work done by GA4GH, I found the avro schema files confusing.
After several working group calls and many emails, I managed t…