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Questions tagged [public-databases]

Use this tag for questions about how to use, download, retrieve, check and browse public databases.

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7 votes
3 answers
5k views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
Peter's user avatar
  • 2,634
7 votes
2 answers
2k views

How to select a cutoff for interaction confidence in STRINGdb?

I have a list of 100 genes that are called as hits in a genetic screening. I want to have a network of the interactions between the proteins of these 100 genes. I am using both STRINGdb web and its R ...
plat's user avatar
  • 1,042
6 votes
1 answer
242 views

Human Cell Atlas - Data availability

A news item from 2017-10-18 on the website of the Human Cell Atlas states: In addition, the consortium today also announced the impending release of gene expression profiles from the first one ...
Gregor Sturm's user avatar
4 votes
1 answer
1k views

Missing data mappings in mygene.info while trying to convert Genes Ensembl Ids to Entrez Ids

I need to convert a lot of Ensembl Ids to the relative counterpart in Entrez (e.g., ENSG00000157764 > 673). I found mygene.info ...
floatingpurr's user avatar
2 votes
1 answer
61 views

Get a comprehensive list of virulence factors for certain or all pathogens?

Is there a database with all known proteins/genes of specific pathogens such as Staph aureus and annotated whether it is a known virulence or resistance factor that idealy can be downloaded in table ...
Soerendip's user avatar
  • 1,295
1 vote
1 answer
128 views

How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
Jabbath's user avatar
  • 113