User: poisonAlien
poisonAlien • 2.5k
- Reputation:
- 2,500
- Status:
- Trusted
- Location:
- Asgard
- Website:
- https://github.com/Poi...
- Last seen:
- 1 day, 13 hours ago
- Joined:
- 5 years, 7 months ago
- Email:
- a*********@gmail.com
Cancer genomics
Posts by poisonAlien
<prev
• 304 results •
page 1 of 31 •
next >
0
votes
2
answers
440
views
2
answers
Comment:
C: TMB Tumor Mutation Burden
... I believe standard WXS capture sizes are around 50 mb. (eg; Agilent sure select) ...
written 8 weeks ago by
poisonAlien • 2.5k
0
votes
0
answers
135
views
0
answers
... I am not sure if I understand teh question correctly. But, you should look at one of those multi region WXS/WGS studies. Somatic mutation profile varies a lot within the bulk tumor based on biopsy site. So its pretty heterogeneous. ...
written 8 weeks ago by
poisonAlien • 2.5k
0
votes
1
answer
160
views
1
answers
... Its using Mutect2 under the hood for variant calling and doing LOT of filtering to remove possible FPs and gremline variants - which is GOOD. I think you should try it! ...
written 12 weeks ago by
poisonAlien • 2.5k
0
votes
1
answer
160
views
1
answers
... If you have only tumor samples, no matter how much of a sophisticated algorithm you use - there is always an uncertainty associated with the somatic status of an identified variant. Having said that, MuTect can still call somatic variants without gremline controls. But again you will have to be care ...
written 3 months ago by
poisonAlien • 2.5k
0
votes
1
answer
302
views
1
answers
... There are few other tools. DeconstructSigs estimates loading of known signatures for every sample in the cohort. If you are interested in de-novo you could try [EMu](http://www.sanger.ac.uk/science/tools/emu) and [Mutational Signature framework](https://www.mathworks.com/matlabcentral/fileexchange/3 ...
written 3 months ago by
poisonAlien • 2.5k
0
votes
1
answer
1.1k
views
1
answers
... Try [Here](https://github.com/PoisonAlien/beadAnalyze) ...
written 3 months ago by
poisonAlien • 2.5k
0
votes
0
answers
213
views
0
answers
... Hi,
You're passing MAF object as an input for `SomInaClust_det` function. My guess is it requires MAF file as an input. May be try this and see...
```r
brca_Sominaclust <- SomInaClust_det(maf_brca, calculate_CDS = TRUE, convert_genenames_to_HGNC=FALSE)
``` ...
written 4 months ago by
poisonAlien • 2.5k
0
votes
1
answer
304
views
1
answers
... Hi,
Whether a gene is a driver or not is usually done on large cohorts based on how frequently the gene is mutated. There are algorithms to identify such genes. How many cell lines do you have in your file ?
In case if you're only interested in a particular mutation,
- you will have to look at ...
written 6 months ago by
poisonAlien • 2.5k
1
vote
3
answers
598
views
3
answers
... They are Ensemble Gene IDs. See [here][1] for converting them to Gene symbols.
[1]: http://www.ensembl.org/Help/Faq?id=125 ...
written 6 months ago by
poisonAlien • 2.5k
1
vote
1
answer
679
views
1
answers
... > The "MAF" in vcf2maf refers to "Mutation Annotation Format", which was
> something unncessarily invented and confusingly named for cancer
> genetics.
So true! This also conflicts with [Multiple Alignment Format][1]
[1]: https://cgwb.nci.nih.gov/FAQ/FAQformat.html#format5 ...
written 7 months ago by
poisonAlien • 2.5k
Latest awards to poisonAlien
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Benefits of 150 bp reads over 100 bp reads in RNA-seq
Scholar
4 months ago,
created an answer that has been accepted.
For A: Is there a good manual/tutorial for TreeView?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Benefits of 150 bp reads over 100 bp reads in RNA-seq
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: How to use Samtools to remove reads whose mate does not map as expected
Scholar
6 months ago,
created an answer that has been accepted.
For A: Is there a good manual/tutorial for TreeView?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For questions on rna-seq data analysis
Good Answer
13 months ago,
created an answer that was upvoted at least 5 times.
For A: Next Generation Sequencing
Popular Question
14 months ago,
created a question with more than 1,000 views.
For questions on rna-seq data analysis
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: Is there any better method to find significant SNVs ?
Scholar
14 months ago,
created an answer that has been accepted.
For A: Is there a good manual/tutorial for TreeView?
Popular Question
15 months ago,
created a question with more than 1,000 views.
For questions on rna-seq data analysis
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: Is there any better method to find significant SNVs ?
Good Answer
15 months ago,
created an answer that was upvoted at least 5 times.
For A: Next Generation Sequencing
Scholar
15 months ago,
created an answer that has been accepted.
For A: Is there a good manual/tutorial for TreeView?
Commentator
15 months ago,
created a comment with at least 3 up-votes.
For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Commentator
15 months ago,
created a comment with at least 3 up-votes.
For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Scholar
15 months ago,
created an answer that has been accepted.
For A: Is there a good manual/tutorial for TreeView?
Good Answer
18 months ago,
created an answer that was upvoted at least 5 times.
For A: Next Generation Sequencing
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 982 users visited in the last hour