User: Collin

gravatar for Collin
Collin770
Reputation:
770
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Trusted
Location:
United States
Last seen:
6 hours ago
Joined:
4 years, 4 months ago
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c************@gmail.com

Posts by Collin

<prev • 86 results • page 1 of 9 • next >
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Answer: A: Getting a list of tumor suppressors
... One source is the Cancer Gene Census (https://cancer.sanger.ac.uk/census ), which provides a list of cancer driver genes and has labels for both oncogenes and tumor suppressor genes. If you are interested in one of the many cancer types available from The Cancer Genome Atlas, the driver gene analysi ...
written 2 days ago by Collin770
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Comment: C: Can't open file 'features': [Errno 2] No such file or directory
... Try adding only the path to the directory (i.e. "/home/ateeqanees/Desktop/20_20/2020plus-1.2.2/") instead of the full path to the script. ...
written 6 days ago by Collin770
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Answer: A: Can't open file 'features': [Errno 2] No such file or directory
... I think the 2020plus.py scripts is not found in your current PATH. Enter something like this into your command line or .bash_rc file: export PATH=$PATH:/path/to/2020plus Where /path/to/2020plus is where you downloaded 2020plus on your system. If successful you should be able to type `which 2020plu ...
written 6 days ago by Collin770
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Answer: A: Cancer driver mutations Identification from VCFs
... I would recommend checking out [OpenCRAVAT][1]. You can annotate your variants directly from VCF files to obtain the consequence type, driver mutation predictions (through CHASMplus), and annotate population allele frequencies in case some of your mutation calls may be germline variants. There's als ...
written 12 days ago by Collin770
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Comment: C: Suggested tool or algorithm for accessing pathogenicity and prioritization of so
... Generally, people that study somatic mutations don't use the term Single Nucleotide Polymorphism (SNP), because the term is overloaded with connotation only applicable to germline variants that are inherited. That being said, most somatic point mutations in cancer are single nucleotide changes. In ...
written 13 days ago by Collin770
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Comment: C: Suggested tool or algorithm for accessing pathogenicity and prioritization of so
... I'm not aware of any method for predicting whether an indel mutation will be a cancer driver. Most methods for predicting cancer driver mutations are focused on missense mutations (e.g., my own method CHASMplus or CanDra). So you might have to utilize models that are trained on germline variants (i. ...
written 14 days ago by Collin770
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Comment: C: Interesting things to do with 23andme data
... Another variant annotation alternative is [OpenCRAVAT][1], which can run directly on the 23andMe files. [1]: https://opencravat.org/ ...
written 16 days ago by Collin770
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Answer: A: about snp prediction
... Another alternative is [OpenCRAVAT][1], which is a GUI you can install on your laptop. If you install the dbSNP plugin in OpenCRAVAT, you can enter many rsids and obtain their SIFT score (or a lot of other annotations/predictions). There are no limits on the number of rsids you can submit through th ...
written 21 days ago by Collin770
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Answer: A: Somatic Variant Annotation and Interpretation
... You could check out [OpenCRAVAT][1], which has many annotations related to somatic mutations in cancer. This includes quite a few of the machine learning predictions for driver mutations in cancer, which Kevin pointed out in his post. I personally recommend CHASMplus, but I am a little bit biased si ...
written 29 days ago by Collin770
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Answer: A: Indel Annotation Tools, Not Loss Of Function
... You could check out [OpenCRAVAT][1], it will annotate variants including indels. Unlike tools like annovar, you can run it simply from either the command line or through a graphical user interface. [1]: https://opencravat.org/ ...
written 11 weeks ago by Collin770

Latest awards to Collin

Scholar 4 days ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Scholar 5 days ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Appreciated 15 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 24 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 2.0 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Supporter 2.0 years ago, voted at least 25 times.
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 3.3 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 3.9 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 3.9 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 4.0 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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