Moderator: Cyriac Kandoth

gravatar for Cyriac Kandoth
Cyriac Kandoth4.8k
Reputation:
4,790
Status:
Trusted
Location:
Memorial Sloan Kettering, New York, USA
Website:
https://www.linkedin.c...
Twitter:
icyreaction
Scholar ID:
Google Scholar Page
Last seen:
19 hours ago
Joined:
5 years, 6 months ago
Email:
c*******@gmail.com

I'm a computer scientist that studies the genetics of cancer in search of druggable targets, early diagnoses, and prevention. I intend to stick with this line of research till it becomes obsolete. In the meantime, there's no shortage of work to bring this science to the masses.

Posts by Cyriac Kandoth

<prev • 258 results • page 1 of 26 • next >
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Job: Open positions at the Center for Molecular Oncology, MSKCC, New York
... The [CMO][1] is one of several [Collaborative Research Centers][2] at [MSKCC][3] that help researchers translate their work into real benefits for cancer patients and clinicians. To this end, we interface with investigators across MSKCC, understand their research/clinical questions, and design seque ...
cancer python job sequencing R genetics written 4 months ago by Cyriac Kandoth4.8k
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Answer: A: Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs
... For your final objective, you should not use vcf2maf. The "MAF" in vcf2maf refers to "Mutation Annotation Format", which was something unncessarily invented and confusingly named for cancer genetics. This possible confusion was already disambiguated in [the post](https://www.biostars.org/p/123822) t ...
written 5 months ago by Cyriac Kandoth4.8k
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Answer: A: Getting 1000 Genomes phase one MAF values
... If you already have these [Phase 1 1000 genome VCFs](ftp://ftp.1000genomes.ebi.ac.uk:/vol1/ftp/phase1/analysis_results/integrated_call_sets) downloaded, then the Global Allele Frequency is within `AF` under the `INFO` column. The VCF format is complex, so don't try to write your own code to parse ou ...
written 5 months ago by Cyriac Kandoth4.8k
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Comment: C: Getting 1000 Genomes phase one MAF values
... I see similar "vocabulary bubbles" in people who study cancer genetics (like me) vs people who spent their careers studying genetics of germline/mendelian diseases. Every research institute invents its own vocabulary. Clearly, we don't get out much. :) ...
written 5 months ago by Cyriac Kandoth4.8k
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Comment: C: Karyotypically Ordered Hg19
... Anything within backticks are simply shell commands that run and return with their standard output for Perl to parse. So in this case, you just add one more argument to the Unix `cat` command. Like this - `cat $d/GL* $d/KI*` Btw, I don't recommend using in-line Perl in a production workflow. Beside ...
written 12 months ago by Cyriac Kandoth4.8k
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Answer: A: genome version in cbioportal
... Sorry that this isn't explicit on the portal. All variants in all studies use `GRCh37.p13` loci and alleles. The autosomes and sex chromosome sequences are equivalent to `hg19`, but the mitochondrial DNA sequence is newer. [Click here](https://www.biostars.org/p/119295/#119308) for details. The eff ...
written 15 months ago by Cyriac Kandoth4.8k
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Comment: C: RUN genome music (MuSiC2) error
... 1. What are the instructions you are following? Have you seen this: https://www.biostars.org/p/62793/ 2. Does your system have docker installed? This will nearly obsolete the need for installation. 3. "zlib" is a popular development library, so it makes sense for a root user to install it system-wid ...
written 16 months ago by Cyriac Kandoth4.8k
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Comment: C: TCGA CNV Files
... Can you create a new post for your question. And clarify it with an example of the normal samples you see listed as nocnv. ...
written 17 months ago by Cyriac Kandoth4.8k
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Comment: C: Installation of the MuSiC suite on unsupported Linux distributions
... Note that the lab has since released a [MuSiC2](https://github.com/ding-lab/MuSiC2), which is also [dockerized here](https://hub.docker.com/r/beifang/music). ...
written 17 months ago by Cyriac Kandoth4.8k
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Comment: C: Installation of the MuSiC suite on unsupported Linux distributions
... Thank you both. I've updated the tutorial to use the new URLs of the R tarballs. ...
written 17 months ago by Cyriac Kandoth4.8k

Latest awards to Cyriac Kandoth

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Installation of the MuSiC suite on unsupported Linux distributions
Appreciated 4 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Appreciated 6 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Appreciated 8 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Appreciated 9 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Appreciated 15 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Scholar 15 months ago, created an answer that has been accepted. For A: Selecting TCGA samples by barcode in CG Hub
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Appreciated 17 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Popular Question 22 months ago, created a question with more than 1,000 views. For Installation of the MuSiC suite on unsupported Linux distributions
Scholar 23 months ago, created an answer that has been accepted. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts

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