Questions tagged [data-mining]

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1answer
63 views

RNA-seq gene/transcript read counts database for Mouse

Is there any RNAseq gene/transcript read count database for the mouse? I already know about ARCHS4, looking for some other source. Thank you
7
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2answers
276 views

Are these standard species abbreviations and how to look up others?

Reactome uses a three letter code for each species which are listed below. Are the letter codes used by Reactome a standard? If so is there a web page or download file that can validate the code and ...
1
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0answers
17 views

Viral Load and Antiretroviral Therapy Dataset

My project is on Mathematical Modeling of the relationship between viral load and antiretroviral therapy. Its purely an academic one which is exploratory in nature. Intend using the different ...
-1
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1answer
61 views

How do I get the gene order from genbank file using gene names?

I have a list of gene names which I know are present in a genbank file. I want to order these genes based on the order of their presence in the genbank. This should also account for whether they are ...
8
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2answers
79 views

How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?

I want measure the hydrophobicity of each amino acid within a PDB structure file. Since I have the PDB file I want to consider the 3D information, rather than sequence-only measures such as GRAVY. I ...
2
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1answer
111 views

Is there a way to retrieve ENSEMBL IDs from a search query?

I would like to be able to batch download FASTA files from ENSEMBL. I normally would use the API to download them from the ENSEMBL gene IDs. However, the IDs aren't ones I know, only ones I would get ...
3
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0answers
116 views

Minfi returning incorrect beta values

UPDATE: I found the solution. I was using normalized values and GEO was using raw beta values. I'm trying to link GEOquery and minfi. Specifically I want to obtain beta values from the idat files ...
2
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2answers
69 views

Using data mining of papers in order to derive genomic connections [closed]

Are there any examples of researchers data mining articles and papers (e.g., from pubmed or google scholar) in order to derive relations between genes and diseases?