User: Collin

gravatar for Collin
Collin680
Reputation:
680
Status:
Trusted
Location:
United States
Last seen:
9 hours ago
Joined:
4 years, 1 month ago
Email:
c************@gmail.com

Posts by Collin

<prev • 76 results • page 1 of 8 • next >
1
vote
1
answer
1.6k
views
1
answers
Comment: C: pathogenicity predictors of cancer mutations
... I would recommend my recent method CHASMplus for missense mutations (see https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30154-1 ). It performs better in benchmarking than other methods (even against meta-preditctors), is cancer type-specific, and you can get scores through an easy to use g ...
written 5 months ago by Collin680
0
votes
2
answers
369
views
2
answers
Comment: C: Which Driver-Gene Detecting Software Supports hg38?
... Regarding your initial question, 20/20+ currently (as of 6/29/2019) does not support hg38, but we hope to implement it soon. ...
written 5 months ago by Collin680
1
vote
2
answers
369
views
2
answers
Comment: C: Which Driver-Gene Detecting Software Supports hg38?
... I've been a secret fan of your responsiveness to the BioStars community for a while. I think it's a great service to the bioinformatics community ...
written 5 months ago by Collin680
0
votes
2
answers
369
views
2
answers
Comment: C: Which Driver-Gene Detecting Software Supports hg38?
... Hi, I'm Collin, one of the first authors on the TCGA PancanAtlas drivers paper. When we benchmarked several methods, MutSigCV did ok, but had several cancer types where the results were flagged as substantial outliers compared to all the other methods. We however did not benchmark your method. ...
written 5 months ago by Collin680
0
votes
2
answers
369
views
2
answers
Comment: C: Which Driver-Gene Detecting Software Supports hg38?
... I'm the person that developed 20/20+ and I have moved to another lab. I do still maintain the software. But all improvements are done in my spare time without really any recognition for doing so. I would, however, recommend against "manual data processing pipelines" as such ad hoc approaches are w ...
written 5 months ago by Collin680
0
votes
1
answer
4.5k
views
1
answers
Comment: C: Effect size of a SNP - contribution to genetic variance
... Yes, one would need to add the variance of the epsilon term to get the full variance of Y, Var[Y] = Var[BX] + Var[epsilon]. But the variance of the random noise term wouldn't be considered a genetic influence on the phenotype. ...
written 10 months ago by Collin680
1
vote
4
answers
4.0k
views
4
answers
Answer: A: Benjamini+ Hochberg multiple testing p.adjust R
... TL;DR There is nothing wrong with the output from the p.adjust function using the "BH" method. If you had more p-values that were not as highly similar, the results would generate different "adjusted p-values" from the "BH" method. You can see the exact calculations performed by p.adjust by simply t ...
written 17 months ago by Collin680
1
vote
1
answer
398
views
1
answers
Comment: C: Constructing a mean ROC curve based on 5 iterations
... Yes, I meant to concatenate them into a single vector. Nearly all methods provide a score which is used for ranking. It's odd that it's not provided as output. They may have an internal score that is just not getting returned to the user. You might need to contact the authors or see if you can modif ...
written 17 months ago by Collin680
2
votes
1
answer
398
views
1
answers
Answer: A: Constructing a mean ROC curve based on 5 iterations
... What happens in 5-fold cross-validation is that you train on 4 of the folds and predict on the hold-out fold. This procedure is repeated until all folds have hold-out predictions on them. Given this preamble, you could just concatenate the scores and labels from the 5 hold-out predictions (which sho ...
written 17 months ago by Collin680
1
vote
1
answer
891
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 18 months ago by Collin680

Latest awards to Collin

Appreciated 12 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 21 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 22 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Supporter 22 months ago, voted at least 25 times.
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 3.1 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 3.7 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 3.7 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 3.7 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: 1613 users visited in the last hour