Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl13k
Reputation:
12,950
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
2 hours ago
Joined:
4 years, 8 months ago
Email:
e***********@gmail.com

Outreach Project Leader for Ensembl. I can help you with anything Ensembl-related (or find someone who can).

Posts by Emily_Ensembl

<prev • 854 results • page 1 of 86 • next >
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Answer: A: Test of selection for gene variants with in a species
... Usually you use a [Hardy-Weinburg equilibrium][1] to identify if a variant is under selection. In a randomly mating population where the variant is not under selection the following should be true: p^2 + 2pq + q^2 = 1 Where p is the frequency of allele 1 and q is the frequency of allele 2. ...
written 4 hours ago by Emily_Ensembl13k
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Answer: A: Finding RNA sequences for a list of genes
... You can do this with BioMart. [Help video to get you started][1]. Filter by your list of gene names, get the cDNA (or even 5' UTR) sequence as attributes. [1]: https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwi6z8KrmPzWAh ...
written 1 day ago by Emily_Ensembl13k
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Comment: C: Error accessing ensembl biomart via BiomaRt R package
... Working fine for me: > library(biomaRt) > listEnsembl() biomart version 1 ensembl Ensembl Genes 90 2 ENSEMBL_MART_MOUSE Mouse strains 90 3 snp Ensembl Variation 90 4 regulation Ensembl Regulati ...
written 7 days ago by Emily_Ensembl13k
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Comment: C: Cosmic Database using BioMart
... You might be best downloading the VCF then using [vcf-tools][1] to filter [1]: https://vcftools.github.io/perl_module.html ...
written 8 days ago by Emily_Ensembl13k
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Answer: A: Cosmic Database using BioMart
... You use the Ensembl variation somatic variation database to access COSMIC data: cosmicMart = useEnsembl (biomart="snp", dataset = hsapiens_snp_som") If you're looking to download the whole COSMIC database, BioMart is not a suitable way to do this. Please download the somatic VCF files from the ...
written 9 days ago by Emily_Ensembl13k
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Answer: A: How to find orthologous intergenic regions?
... You could find the [precomputed alignments][1] in Ensembl Plants. [1]: http://plants.ensembl.org/Arabidopsis_thaliana/Location/Compara_Alignments?r=1:8001-18000 ...
written 9 days ago by Emily_Ensembl13k
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Answer: A: How to get coordinates from HGVSc, HGVSp and gene name
... You could put the HGVSc notation into the [Ensembl VEP][1]. [1]: http://www.ensembl.org/info/docs/tools/vep/index.html ...
written 10 days ago by Emily_Ensembl13k
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Comment: C: PhD and MSc positions at KAUST, Thuwal, Saudi Arabia
... I'm assuming women need not apply? ...
written 11 days ago by Emily_Ensembl13k
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Comment: C: PostDoc position at KAUST, Thuwal, Saudi Arabia
... I'm assuming women need not apply? ...
written 11 days ago by Emily_Ensembl13k
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Answer: A: Availability of pre-ensembl information in biomart
... We don't have BioMart for genomes in pre. These are genomes that have not yet been fully processed and do not have the full file structure, which means we don't have the BioMart tables. Crab eating macaque is due to appear in the next Ensembl release, due in December. ...
written 18 days ago by Emily_Ensembl13k

Latest awards to Emily_Ensembl

Popular Question 3 days ago, created a question with more than 1,000 views. For Making bioinformatics help and tutorials open
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Ensembl VEP 89 Output Format
Scholar 10 days ago, created an answer that has been accepted. For A: Ensembl VEP 89 Output Format
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Ensembl VEP 89 Output Format
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Ensembl VEP 89 Output Format
Scholar 22 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Appreciated 23 days ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Popular Question 28 days ago, created a question with more than 1,000 views. For Making bioinformatics help and tutorials open
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Appreciated 29 days ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 5 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Appreciated 8 weeks ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 8 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: (Where) can I download the Ensembl cross reference database?
Scholar 8 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 9 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?

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