User: D. Puthier

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D. Puthier320
Reputation:
320
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Location:
France/Marseille/Inserm
Last seen:
9 months ago
Joined:
9 years, 10 months ago
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Posts by D. Puthier

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Emboss Shared Libraries
... If you are running ubuntu you should try to install EMBOSS through `apt-get`. sudo apt-get install emboss-data emboss-doc embassy-domainatrix embassy-domalign ...
written 9.5 years ago by D. Puthier320 • updated 9 months ago by RamRS27k
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Comment: C: Fundamentals Of Designing Biological Databases?
... You are probably right. The method is a little bit old fashioned and one should better learn a more universal language. However MERISE is very straightforward and fits with most conventional database modeling problems. ...
written 9.6 years ago by D. Puthier320
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Comment: C: Hypergeometric Test R/Bioconductor
... I think also that an example file would be necessary. ...
written 9.6 years ago by D. Puthier320
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Answer: A: Overrepresentation Analysis For Microrna Binding Sites In Utrs?
... Perhaps CORNA (R/BioC). ...
written 9.6 years ago by D. Puthier320
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Comment: C: Fundamentals Of Designing Biological Databases?
... Just another thing. In some cases you are tempted to de-normalized because of performance issues. Just keep in mind that there are several ways of improving the overall performance of a query (where, join on multiple keys, temporary table, no imbricated select, procedures,...). ...
written 9.6 years ago by D. Puthier320
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Answer: A: Fundamentals Of Designing Biological Databases?
... Concerning database modeling the easiest way to get something with few redondancy (that is "normalized") and reasonable performance is to use the MERISE method (I think this is the french equivalent to E/A modelling). You will have to draw a conceptual data model (MCD) (a diagram with entities and a ...
written 9.6 years ago by D. Puthier320
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Comment: C: Fundamentals Of Designing Biological Databases?
... "Indexing all foreign keys is just wrong advice". Yes. Especially, if one works with MyISAM table (the most popular mySQL engine) where a foreign key has no meaning for the engine. ...
written 9.6 years ago by D. Puthier320
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Answer: A: Hypergeometric Test R/Bioconductor
... The format of your files is not very clear. If these are tabulated files you should use the `read.table` function as the `selected` object is an instance of class vector and should not if you have multiple columns (Expressed genes with `Probes_id`,`entrez_gene_id`,`symbols`,`P.Value` and `F.C`). So ...
written 9.6 years ago by D. Puthier320 • updated 8 months ago by RamRS27k
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Answer: A: Transfac - Finding Transcription Factor Binding Sites?
... Have a look at the courses given by J. Van Helden. Especially this one. Next you can download Transfac academic version from here. Finally, using the RSAT web serveur, you should be able do get the promoter region of your gene of interest to scan it using any PWM. ...
written 9.7 years ago by D. Puthier320

Latest awards to D. Puthier

Scholar 4.4 years ago, created an answer that has been accepted. For A: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Selecting A Column From A File Based On Column Name
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: Fundamentals Of Designing Biological Databases?
Teacher 9.4 years ago, created an answer with at least 3 up-votes. For A: Fundamentals Of Designing Biological Databases?
Teacher 9.6 years ago, created an answer with at least 3 up-votes. For A: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Appreciated 9.7 years ago, created a post with more than 5 votes. For A: Tumor Rna Expression Databases
Good Answer 9.7 years ago, created an answer that was upvoted at least 5 times. For A: Tumor Rna Expression Databases
Teacher 9.7 years ago, created an answer with at least 3 up-votes. For A: Tumor Rna Expression Databases
Teacher 9.9 years ago, created an answer with at least 3 up-votes. For A: Self-Learning Gene-Expression K-Means Clustering In R

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