Questions tagged [data-mining]
Initial process of data analysis often used to define the hypothesis for subsequent analysis
10
questions
1
vote
0
answers
26
views
How to investigate the correlation between transcript and protein abundance?
Our study shows that gene A knockout will down-regulate cell cycle-related genes in some cell lines. My aim is to understand whether cell cycle-related genes are down regulated on the transcriptional ...
- 101
2
votes
0
answers
39
views
Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?
When we use antismash command with the genome sequence file as follows:
antismash GCA_002095535.1_ASM209553v1_genomic.gbff
it screens the genome for all the ...
- 21
1
vote
1
answer
85
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
- 351
8
votes
2
answers
624
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 ...
- 315
1
vote
0
answers
23
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 investigation which is exploratory in nature.
Question I am seeking a ...
- 111
-1
votes
1
answer
167
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 ...
- 945
8
votes
2
answers
188
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 ...
- 507
2
votes
1
answer
188
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 ...
- 439
3
votes
0
answers
168
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 ...
- 83
2
votes
2
answers
71
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?
- 1,417