User: Collin

gravatar for Collin
Collin680
Reputation:
680
Status:
Trusted
Location:
United States
Last seen:
10 hours ago
Joined:
4 years, 3 months ago
Email:
c************@gmail.com

Posts by Collin

<prev • 77 results • page 2 of 8 • next >
1
vote
1
answer
939
views
1
answers
Comment: C: Computing ROC curves without scores
... the Precision-Recall curve basically assesses what your saying. Precision is the fraction of predicted positives that are labeled as true positive (also known as positive predictive value). You can always mark with a dot the precise point on the curve that equals the top 100 genes. This would give y ...
written 19 months ago by Collin680
1
vote
1
answer
939
views
1
answers
Comment: C: Computing ROC curves without scores
... I disagree on the point that ROC curves doesn't give the following information "how many genes you need to take to get a given sensitivity value". You can in fact pick the corresponding number of genes from the threshold that produces X% sensitivity on the ROC curve (and understand what the false po ...
written 19 months ago by Collin680
1
vote
1
answer
939
views
1
answers
Comment: C: Computing ROC curves without scores
... Yep it is a network-based gene prioritization approach. Based on their paper, it does create a score that it uses to rank the genes. However, from their user documents they don't provide it as an output. So from a practical perspective, like Jean-Karim noted, you likely have to use the rank of the g ...
written 20 months ago by Collin680
1
vote
1
answer
939
views
1
answers
Comment: C: Computing ROC curves without scores
... That's odd that the program doesn't give you a numerical value. Without a numerical value you have no way of knowing whether two genes were tied on a prioritization assessment. So you likely will have to just assume no ties. I think the most explainable way is what you propose, that is you construct ...
written 20 months ago by Collin680
0
votes
1
answer
435
views
1
answers
Comment: C: Alternative tools replace MutDB to predict consequences of deleterious SNV
... Could you clarify whether you are interested in germline mutations or somatic mutations? The table you include has many cancer-specific methods, but the semantic "deleterious SNV" would suggest you are interested in germline mutations. ...
written 23 months ago by Collin680
2
votes
1
answer
435
views
1
answers
Answer: A: Alternative tools replace MutDB to predict consequences of deleterious SNV
... You could use scores from the VEST algorithm (PMID: 23819870). It's pretty easy to score SNVs by just submitting them to the CRAVAT webserver (http://www.cravat.us/CRAVAT/, PMID: 29092935). In one of the latest papers to benchmark performance, VEST is among the best (PMID: 29179779). ...
written 23 months ago by Collin680
3
votes
2
answers
647
views
2
answers
Comment: C: Why GWASs cannot speculate what kind of mutation the SNP would cause?
... My assumption is that generally the "lead" SNPs identified as most significant in GWAS are not necessarily the actual causal SNP because of linkage disequilibrium. Therefore trying to ascertain a function or effect of those SNPs would be misleading. I believe they generally try to do further studie ...
written 23 months ago by Collin680
0
votes
1
answer
765
views
1
answers
Comment: C: 2020+ installation problems:
... The simulations are mostly useful for 20/20+. What are you intending to do that isn't already done in the pipeline for 20/20+ (2020plus.readthedocs.io/en/latest/ )? ...
written 2.1 years ago by Collin680
1
vote
1
answer
765
views
1
answers
Comment: C: 2020+ installation problems:
... Are you missing any of the following files: genes.fa, genes.bed, or mutations.txt (FASTA, BED, or mutation file)? The instructions on the probabilistic2020 web site (http://probabilistic2020.readthedocs.io/en/latest/tutorial.html ) are meant for three hypothetical files, and actually need to be pro ...
written 2.1 years ago by Collin680
0
votes
1
answer
765
views
1
answers
Comment: C: 2020+ installation problems:
... What python version and operating system are you using? ...
written 2.1 years ago by Collin680

Latest awards to Collin

Appreciated 14 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 22 months ago, created a question with more than 1,000 views. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Supporter 23 months ago, voted at least 25 times.
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 3.2 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 3.8 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 3.8 years ago, asked a question with at least 3 up-votes. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Scholar 3.9 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1129 users visited in the last hour