User: Noushin N

gravatar for Noushin N
Noushin N580
Reputation:
580
Status:
Trusted
Location:
Baltimore, MD
Scholar ID:
Google Scholar Page
Last seen:
5 months, 3 weeks ago
Joined:
7 years, 1 month ago
Email:
n**************@gmail.com

Posts by Noushin N

<prev • 94 results • page 1 of 10 • next >
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Comment: C: Ensembl REST API Optional Parameters
... Thanks, https://www.biostars.org/u/7019/ ! The tutorials were great. For future reference of myself and others, here is an example of how one would add protein domain annotation and uniprot protein ids to vep results for an input specified in genomic coordinates: ``` server <- "http://grch37.r ...
written 6 months ago by Noushin N580
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Comment: C: Ensembl REST API Optional Parameters
... Thank you! I am using this in an R script and using POST endpoint. ...
written 7 months ago by Noushin N580
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Ensembl REST API Optional Parameters
... Hello, Can anyone please share an example of how one can specify optional parameters when using VEP through Ensembl REST API? I am following the examples on this [page][1] and would like to limit the results to those from canonical transcripts, and only return the maximum allele frequency in any po ...
ensembl vep written 7 months ago by Noushin N580 • updated 6 months ago by Emily_Ensembl21k
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Comment: C: Rsamtools mpileup discrepancy
... Thank you for your input. I have considered this possibility as well. However, given that Rsamtools is supposedly ["an interface to the samtools"][1] , I wonder why the default behavior is different between the two and how we can make them match. [1]: https://bioconductor.org/packages/release/bi ...
written 7 months ago by Noushin N580
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Rsamtools mpileup discrepancy
... Hi everyone, I was wondering if you can share any tips to mitigate the following issue. I am interested in getting the count of reads carrying the reference and alternate reads at a number of genomic positions, which is a straightforward mpileup question. However, I have noticed that when I run the ...
R samtools written 7 months ago by Noushin N580
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Comment: C: Annotation with Ensembl REST API
... Thanks so much for the prompt follow up, https://www.biostars.org/u/7019/ . I will try again within a couple of days and see how it looks. ...
written 8 months ago by Noushin N580
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Comment: C: Annotation with Ensembl REST API
... Tagging: https://www.biostars.org/u/7019/ ...
written 8 months ago by Noushin N580
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Annotation with Ensembl REST API
... I would like to annotate a set of variants in terms of their protein consequence inside a piece of R code. I have tried to model my code after the [example][1] from ensembl REST API, but encounter the following error: Error in curl::curl_fetch_memory(url, handle = handle) : Could not resolv ...
ensembl api R written 8 months ago by Noushin N580 • updated 8 months ago by Emily_Ensembl21k
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Intra-tumor Heterogeneity / Mutation Cellular Fraction in TCGA Data
... Hello, I was wondering if anyone is aware of an online resource where information on mutation cancer cell fraction estimates for TCGA samples can be retrieved. I am aware of two excellent studies which have performed the exact analysis to derive the above. But I cannot locate the corresponding va ...
heterogeneity tcga written 18 months ago by Noushin N580
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Comment: A: How to find patient sample.type in TCGA-PRAD ?
... You can make a table that translates the numeric code to the sample types listed [here][1]. [1]: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes ...
written 2.1 years ago by Noushin N580

Latest awards to Noushin N

Great Question 6 months ago, created a question with more than 5,000 views. For Samtools Index Segmentation Fault
Popular Question 15 months ago, created a question with more than 1,000 views. For Calling CNA from aCGH: Thresholding?
Popular Question 16 months ago, created a question with more than 1,000 views. For Calling CNA from aCGH: Thresholding?
Appreciated 17 months ago, created a post with more than 5 votes. For A: identifying TP53 germline mutations which are also in tumor cells.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For NGS preprocessing pipleine for ion torrent data
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Calculating Variant Allele Frequency
Great Question 2.3 years ago, created a question with more than 5,000 views. For Samtools Index Segmentation Fault
Popular Question 2.4 years ago, created a question with more than 1,000 views. For NGS preprocessing pipleine for ion torrent data
Scholar 2.5 years ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Calculating Variant Allele Frequency
Scholar 2.5 years ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Calculating Variant Allele Frequency
Popular Question 2.8 years ago, created a question with more than 1,000 views. For NGS preprocessing pipleine for ion torrent data
Appreciated 3.0 years ago, created a post with more than 5 votes. For Somatic mutation calling without matched normal
Scholar 3.6 years ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Scholar 3.9 years ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Somatic mutation calling without matched normal
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Somatic Mutation Phasing
Student 5.1 years ago, asked a question with at least 3 up-votes. For Somatic mutation calling without matched normal
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Supporter 6.3 years ago, voted at least 25 times.

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