User: ivivek_ngs

gravatar for ivivek_ngs
ivivek_ngs4.6k
Reputation:
4,620
Status:
Trusted
Location:
Seattle,WA, USA
Website:
https://github.com/vd4...
Twitter:
@ivivek87
Last seen:
4 hours ago
Joined:
5 years, 6 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 now I want to drive the improvements in the field. 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 Target discovery employing Integrative computational systems medicine approach.

Posts by ivivek_ngs

<prev • 932 results • page 1 of 94 • next >
1
vote
2
answers
480
views
2
answers
Comment: C: Data selection for RNA-seq data analysis
... Well if you follow any omics paper related to Kidney or even Cancers of which biopsies are limited and rare you will get the approach 2. I am not a big fan of approach 2 but sometimes it is what you need to do with a grain of salt. Approach 2 is totally agnostic of any robust statistical assumption ...
written 2 days ago by ivivek_ngs4.6k
0
votes
2
answers
2.5k
views
2
answers
Comment: C: RNA seq results as fpkm
... Still we see papers publishing things in FPKM normalization. Alas! ...
written 6 months ago by ivivek_ngs4.6k
0
votes
0
answers
4.2k
views
0
answers
Comment: C: Clustering of DAVID gene enrichment results from gene expression studies
... Very useful and a great way to look that data will multi feature. Will give it a try. Great resource to be bookmarked. ...
written 8 months ago by ivivek_ngs4.6k
0
votes
0
answers
301
views
0
answers
Comment: C: GeNets: a unified web platform for network-based genomic analyses
... Sure, please do. I was not aware of this tag. Thanks ...
written 8 months ago by ivivek_ngs4.6k
2
votes
0
answers
301
views
0
answers
News: GeNets: a unified web platform for network-based genomic analyses
... A new [tool][1] is up from the Broad Institute. It is named as **GeNets** Just had a look to it today. Seems very comprehensive and wide range of things catering to both network and pathway analysis. Also the tutorials and website have a very aesthetic feel. I would like the community to take a look ...
pathways news visualization networks rna-seq written 8 months ago by ivivek_ngs4.6k • updated 8 months ago by genomax62k
0
votes
2
answers
3.7k
views
2
answers
Comment: C: TMB Tumor Mutation Burden
... I would go with either the GATK CallableLoci or the capture size , that should be the one in use rather than something arbitrary. ...
written 8 months ago by ivivek_ngs4.6k
0
votes
1
answer
350
views
1
answers
Comment: C: Noise Analysis for RNAseq Data
... what do you mean by unique number? Are you referring to mean-variance trend plot and then calculating the scaling factor based on your normalizing factor? ...
written 9 months ago by ivivek_ngs4.6k
0
votes
1
answer
350
views
1
answers
Comment: C: Noise Analysis for RNAseq Data
... Some pointers: 1. Well you need numbers/replicates first, for each techniques to interpret errors/biases/noises. Do you have that? 2. If so then look for density plot of the data and then go for your threshold to remove genes with zero or low counts depending upon the distribution. 3 ...
written 9 months ago by ivivek_ngs4.6k
1
vote
2
answers
398
views
2
answers
Comment: C: Merging specific columns from different txt files in a unit file
... simple search and you get multiple hits as to how you can use multiple bam files with featureCounts and generate one matrix with all samples for a expression matrix. [https://www.biostars.org/p/277316/][1] [https://support.bioconductor.org/p/64932/][2] Finally read the [manual of featureCounts][3 ...
written 9 months ago by ivivek_ngs4.6k
0
votes
0
answers
380
views
0
answers
Comment: C: VCF SNP analysis
... so if you are trying to find mutations or variants from RNASeq then samtools workflow or STAR/GATK workflow should be fine. I personally like STAR/GATK owing to the statistical model and robustness that you can add to it. Having said that, once you have VCF you can always plot stats to see how many ...
written 9 months ago by ivivek_ngs4.6k

Latest awards to ivivek_ngs

Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Great Question 11 weeks ago, created a question with more than 5,000 views. For Variant Reduction Using Annovar
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: ICGC Variant Calling Pipelines
Scholar 5 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Teacher 5 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
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 7 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Appreciated 9 months ago, created a post with more than 5 votes. For A: ICGC Variant Calling Pipelines
Appreciated 10 months ago, created a post with more than 5 votes. For A: ICGC Variant Calling Pipelines
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: ICGC Variant Calling Pipelines
Student 12 months ago, asked a question with at least 3 up-votes. For Rna-Seq Data Normalization With Spike-In Using Deseq
Popular Question 15 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 753 users visited in the last hour