User: Dave

gravatar for Dave
Dave70
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Japan
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4 years ago
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7 years, 7 months ago
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Posts by Dave

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Rank-based GO enrichment packages for R?
... Thanks for trying to answer, but I am afraid you did not really understand the question: As I wrote, I am aware of the many R packages to do GO enrichment. The problem is that all the ones I have found so far (and indeed, the one you linked) are for gene set enrichment. They require you to specify ...
written 4.2 years ago by Dave70
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Rank-based GO enrichment packages for R?
... As stated in the title: I am looking for a rank-based (or possibly score-based, but I am not sure any such methods exist) tool for GO enrichment that can be used from R. All the packages I have found so far (e.g. TopGO) only offer enrichment based on a selected set of genes (possibly obtained throu ...
R go written 4.2 years ago by Dave70 • updated 4.2 years ago by Ido Tamir5.0k
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Comment: C: Best HMM library for bioinformatics
... Thanks a lot for the suggestion. Indeed, I just had a look at stochHMM and it looked impressive (and very nicely documented) until I ran into that mention: "The Baum-Welch, Viterbi Training, and other forms of unsupervised training are not supported by StochHMM"... Unfortunately, that is a pretty bi ...
written 4.9 years ago by Dave70
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Best HMM library for bioinformatics
... Despite this being a rather basic question, I was not able to find a previous post in the archives (hope I did not miss it). I am looking at implementing a markovian model similar to HMMER's markov profiles (but different enough that hhpred will not do the job) and was looking at available librarie ...
hmm java C tool python written 4.9 years ago by Dave70 • updated 4.9 years ago by a.polo88100
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Speeding Up Psipred (Or Finding A Better Locally-Run Alternative)
... I know there have already been a few general questions about tools for secondary-structure prediction, but hopefully mine is a bit more specific. I am currently using psipred as part of a pipeline where I need secondary-structure and wondering if there is any way I can speed up the process a little ...
protein-structure written 6.2 years ago by Dave70 • updated 6.0 years ago by Hamish3.1k
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Comment: C: Is Omim No Longer Available As Structured Data?
... This copyright restriction has been true from the start. The problem about now is not just that they don't provide a programmatic way to access the data, it's that they don't even provide that data (the web version is not as complete as the old XML was. ...
written 7.6 years ago by Dave70
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Comment: C: Is Omim No Longer Available As Structured Data?
... I had missed this part (their doc for eutils still clearly give examples to use OMIM). So the short answer is no, there is no XML access to OMIM any more. ...
written 7.6 years ago by Dave70
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Is Omim No Longer Available As Structured Data?
... One of our project used to query OMIM data as XML through NCBI's efetch utility, as described here for example: What is the best way to interact programmatically with OMIM? However, it seems the service has stopped functioning a few months ago. It now simply returns the following error: Databa ...
ncbi api written 7.6 years ago by Dave70 • updated 7.6 years ago by Mary11k

Latest awards to Dave

Appreciated 6.2 years ago, created a post with more than 5 votes. For Is Omim No Longer Available As Structured Data?
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Is Omim No Longer Available As Structured Data?
Student 6.2 years ago, asked a question with at least 3 up-votes. For Is Omim No Longer Available As Structured Data?

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