User: B. Arman Aksoy

gravatar for B. Arman Aksoy
B. Arman Aksoy1.2k
Reputation:
1,170
Status:
Trusted
Location:
New York, NY
Website:
http://ergoso.me
Scholar ID:
Google Scholar Page
Last seen:
1 year, 10 months ago
Joined:
7 years, 12 months ago
Email:
a*****@gmail.com

Posts by B. Arman Aksoy

<prev • 68 results • page 1 of 7 • next >
0
votes
1
answer
1.6k
views
1
answers
Comment: C: SciClone: How to interpret Coverage vs VAF plots
... thanks, Chris — much appreciated! ...
written 3.2 years ago by B. Arman Aksoy1.2k
4
votes
1
answer
1.6k
views
1
answer
SciClone: How to interpret Coverage vs VAF plots
... I am currently in the process of trying to understand what each clonality inference does under the cover and while doing that I realize that both the SciClone paper and the R-library feature [a multi-panel plot][1] to show Coverage vs VAF (Variant Allele Frequency) nicely aligned with a VAF histogra ...
sciclone coverage sequencing written 3.2 years ago by B. Arman Aksoy1.2k • updated 3.2 years ago by Chris Miller20k
7
votes
0
answers
2.1k
views
0
answers
Forum: The Road to Independence - A blog post series for graduate students seeking early independence
... Hi all, I have recently been thinking a lot about applying to independent post-doc fellowships, a.k.a early independent positions. These positions are already quite scarce and there is not much information out there on these fellowships or how to properly apply for one. I decided to address this la ...
career early independence forum fellowship written 4.5 years ago by B. Arman Aksoy1.2k • updated 4.5 years ago by RamRS21k
5
votes
1
answer
3.5k
views
1
answers
Answer: A: Per Cancer Bulk Download from CBioPortal
... cBioPortal, unfortunately, does not support such bulk-download requests. As you also mentioned, you can download these data sets from TCGA; since you want to work with higher-level data, I suggest you download the data from Firehose analysis results instead of using TCGA's raw data download site: h ...
written 4.5 years ago by B. Arman Aksoy1.2k
0
votes
2
answers
1.8k
views
2
answers
Comment: C: Common target genes
... Right now it is not possible to request another identifier through the web service, but the last example which produces EXTENDED_BINARY_SIF, will help you get this. In that file, in addition to the standard identifiers, you also have access to other identifiers associated with the node (like HGNC, E ...
written 4.7 years ago by B. Arman Aksoy1.2k
1
vote
2
answers
1.8k
views
2
answers
Answer: A: Common target genes
... You can accomplish this via the Pathway Commons 2 web service. The query type of interest to you is the commonstream in either upstream or downstream directions. For example, the following gives you the common downstream of EGFR and ERBB2: http://www.pathwaycommons.org/pc2/graph?source=EGFR,ERBB2&a ...
written 4.7 years ago by B. Arman Aksoy1.2k
3
votes
2
answers
2.9k
views
2
answers
Answer: A: Looking databases for experimentaly validated miRNA-target interaction
... miRTarBase is yet another great resource for such data. ...
written 4.8 years ago by B. Arman Aksoy1.2k
2
votes
2
answers
3.3k
views
2
answers
Answer: A: Current sources for pathway data/gene sets
... It doesn't have KEGG and Biocarta, but you can download the GSEA filesfor various data sources from the latest Pathway Commons 2 web service: http://www.pathwaycommons.org/pc2/downloads.html These files contain UniProt IDs, though. You might need to map these back to some other type of id dependin ...
written 4.8 years ago by B. Arman Aksoy1.2k
2
votes
2
answers
2.8k
views
2
answers
Answer: A: BIOPAX format : Pathway analysis
... There are no web-based BioPAX visualizers available right now. Since you specifically asked for this, I will skip installable softwares such as ChiBE, Cytoscape 3.0 and PathVisio, all of which can visualize BioPAX pathways and allow you export static images. One workaround this problem is to conver ...
written 4.8 years ago by B. Arman Aksoy1.2k
0
votes
1
answer
4.4k
views
1
answers
Answer: A: How To Compare Gene Expression And Methylation Level Of A Gene
... Selection of the probes is a hard problem; the way TCGA does it to assign a methylation score for each is to correlate all probe values in the proximity of a gene with the gene expression, and pick the one that best negative correlation. This is of course having some phenotype of interest in mind, i ...
written 5.1 years ago by B. Arman Aksoy1.2k

Latest awards to B. Arman Aksoy

Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Extracting Curated Protein-Protein Interactions From Reactome
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Extracting Curated Protein-Protein Interactions From Reactome
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Network Biology
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Tcga Mirnaseq Differential Analysis: U-Test Or Edger-Like Approaches On Rpm Values
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: Extracting Curated Protein-Protein Interactions From Reactome
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: How Can We Get Tissue Specific Genes?
Good Answer 3.8 years ago, created an answer that was upvoted at least 5 times. For A: How Can We Get Tissue Specific Genes?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Tcga Mirnaseq Differential Analysis: U-Test Or Edger-Like Approaches On Rpm Values
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Network Biology
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Network Biology
Guru 4.5 years ago, received more than 100 upvotes.
Scholar 4.9 years ago, created an answer that has been accepted. For A: How To Compare Gene Expression And Methylation Level Of A Gene
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Network Biology
Supporter 5.1 years ago, voted at least 25 times.
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Predict Oncogenic Potential Of Snv
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Network Biology
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: N-Gram Plots Using Pmc Or Pubmed Abstracts
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Extracting Curated Protein-Protein Interactions From Reactome
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Know Of Any Personal Fellowships, But Not Postdoctoral Positions, In Bioinformat
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: What Is The Meaning Of Reactome'S 'Set To Member' Reaction Attribute?
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: How Can We Get Tissue Specific Genes?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1922 users visited in the last hour