User: ivivek_ngs

gravatar for ivivek_ngs
ivivek_ngs5.0k
Reputation:
4,960
Status:
Trusted
Location:
Seattle,WA, USA
Website:
https://github.com/vd4...
Twitter:
@ivivek87
Last seen:
3 days, 7 hours ago
Joined:
6 years, 12 months ago
Email:
v*******@gmail.com

I did my PhD in the field of Cancer Computational Medicine employing NGS tools(publicly available) or ad-hoc development and analyzing them. Mostly I did bench-marking of tools till I find the best fit for the heterogeneous cancer data. I worked on integrating multi omics data and briefly ventured in field of single cell which is pretty interesting to me as of now (still working on it as per requirement in the industry).

Battling with two of my worst fears Biology and Computer Science to give life a better meaning. My first fear made me push to get the PhD and my second help me learn to solve problems amassing big-data, in an unbiased data-driven way, thus letting me earn my PhD. Now I want to drive the improvements in the field of healthcare bridging both Biology and Computer Science. I enjoy the interdisciplinary terms Bioinformatics or Computational Biology, but in heart  and mind, I am a Systems Biologist who loves learning data-shapes, distributions , what it provides as features and these can help formulate better biological queries and also address apriori queries or new ones. The challenge in life science and technology drives me and so I am pursuing the research field.

Everyday is a new learning and knowledge is never ending.

Biostars helped me learn all along and now with my experience and learning am happy to help others. 

Creating automated pipeline/workflow scripts for easy usage of different seq technologies. I am passionate about integration of multi-omics data in varied therapeutic areas involving human patients data-sets and leveraging the power of pre-clinical animal models together for target discovery. 

I am interested in Precision and Personalized Medicine and would like to use my skills in the same with translational NGS technologies for addressing problems related to diseases. Currently working in industry in Biomarkers & Target Discovery employing Integrative Computational Systems Medicine approach.

Posts by ivivek_ngs

<prev • 966 results • page 1 of 97 • next >
0
votes
1
answer
92
views
1
answers
Answer: A: targeted RNA-Seq best practices
... Hi, there is another technology that you can use if you don’t want to validate your DE genes panel in another cohort or same but another replicates. This is via multi panels from a technology call NanoString. They can profile few custom panels but also have their own. Probes are already available bu ...
written 6 days ago by ivivek_ngs5.0k
2
votes
1
answer
113
views
1
answers
Answer: A: Seurat :Violin plot showing relative expression of select differentially express
... Hi, The above plot isn’t from Seurat AFAIK, it is from `scanpy()`. Last time I checked this multi gene plot function wasn’t available but one can play around and generate it. Ming has a blog post with code around `ggplot()`. If you are not familiar with `python` and underlying packages of single ce ...
written 6 days ago by ivivek_ngs5.0k
0
votes
0
answers
4.2k
views
0
answers
Comment: C: n.sv number for batch effects in RNA-seq
... Hi both, Apologies for the late reply. I have replied to it [here][1]. [1]: https://www.biostars.org/p/262616/#442533 ...
written 8 weeks ago by ivivek_ngs5.0k
0
votes
1
answer
9.5k
views
1
answers
Comment: C: how to display multiple row annotations on pheatmap
... I would encourage you to search the error in this forum or Google or StackOverflow. In case you do not find it. Please write a new post in those mentioned forums detailing your problem scope, code snippet, and error, so that we can better assist. ...
written 8 weeks ago by ivivek_ngs5.0k
1
vote
0
answers
4.8k
views
0
answers
Comment: C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext
... Hi, Apologies for the late reply. `plPCA()` was basically a wrapper around the PCA function developed in my former lab. Any standard PCA function or packages having PCA should work. There are currently multiple exploratory packages available in BioConductor or CRAN for performing PCA or any other st ...
written 8 weeks ago by ivivek_ngs5.0k
0
votes
3
answers
6.0k
views
3
answers
Comment: C: PCA tpm fpkm
... Apologies for the late reply. There are many such Biostar examples floating. In short, these are for visualization purposes. Correcting for batch on your FPKM/TPM and looking into PCA/MDS. This only guides us with our data-driven vs hypothesis driven goals. For DGElist or any differential analysis, ...
written 12 weeks ago by ivivek_ngs5.0k
0
votes
3
answers
6.0k
views
3
answers
Comment: C: PCA tpm fpkm
... I second that answer to being careful with PCA. We do it but often we do not try to understand the pros and cons of using it in array/RNASeq data. The underlying mathematics and assumptions need to be well thought for any dimension reduction methods. Again given data space is not big, one also need ...
written 12 weeks ago by ivivek_ngs5.0k
0
votes
4
answers
4.4k
views
4
answers
Comment: C: How to find out the insert size in RNA seq data
... Yes, I should have updated it, thanks for putting it in the thread. ...
written 13 months ago by ivivek_ngs5.0k
1
vote
0
answers
4.8k
views
0
answers
Comment: C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext
... Glad it worked out now at your end. I should have pointed out the part of Jeff Leek advice( I was indicating the same but I was not that comprehensive out there), since pre-adjustment is only advisable for a visualization perspective but for model they should be incorporated as covariates to not im ...
written 13 months ago by ivivek_ngs5.0k
1
vote
0
answers
4.8k
views
0
answers
Comment: C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext
... Wwell, limma is used for DNA methlylation. Should not be an issue, it is just not the voom transformation. Well in voom you will have the difference since it is for RNASeq, while traditionally limma is for array based works so DNAmethylation fits that bill, in that case your query should be valid. T ...
written 13 months ago by ivivek_ngs5.0k

Latest awards to ivivek_ngs

Scholar 5 days ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Presenting "Role of genomics in cancer" to graduate students from different fiel
Popular Question 5 months ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 8 months ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Presenting "Role of genomics in cancer" to graduate students from different fiel
Popular Question 13 months ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Presenting "Role of genomics in cancer" to graduate students from different fiel
Scholar 17 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Great Question 20 months ago, created a question with more than 5,000 views. For Variant Reduction Using Annovar
Appreciated 20 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: ICGC Variant Calling Pipelines
Scholar 22 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Presenting "Role of genomics in cancer" to graduate students from different fiel

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1389 users visited in the last hour