User: vchris_ngs

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vchris_ngs4.5k
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Seattle,WA, USA
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https://github.com/vd4...
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@vchris21
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I did my PhD in the field of Cancer Biology employing NGS tools(publicly available) or ad-hoc development and analysing them. Mostly I do benchmarking of tools till I find the best fit for the heterogeneous cancer data. I work on integrating multi omics data and slowly now am venturing in field of single cell which is pretty interesting to me as of now. 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 scripts for easy usage of different seq technologies.

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 Omics Drug Discovery.

Posts by vchris_ngs

<prev • 931 results • page 1 of 94 • next >
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Comment: C: RNA seq results as fpkm
... Still we see papers publishing things in FPKM normalization. Alas! ...
written 2 days ago by vchris_ngs4.5k
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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 weeks ago by vchris_ngs4.5k
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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 weeks ago by vchris_ngs4.5k
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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 weeks ago by vchris_ngs4.5k • updated 8 weeks ago by genomax54k
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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 12 weeks ago by vchris_ngs4.5k
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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 3 months ago by vchris_ngs4.5k
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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 3 months ago by vchris_ngs4.5k
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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 3 months ago by vchris_ngs4.5k
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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 3 months ago by vchris_ngs4.5k
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Answer: A: Drug set enrichment analysis
... I would list out [DGIdb][1], probably if you have not come across. Take a look at it. The one of TIGEM is good as well but everything depends on how well the resources are updated. [Opentargets][2] should have also the functionality, if I am not wrong. Check it once or write their support. Now si ...
written 3 months ago by vchris_ngs4.5k

Latest awards to vchris_ngs

Commentator 11 days ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 6 weeks ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Appreciated 3 months ago, created a post with more than 5 votes. For A: ICGC Variant Calling Pipelines
Appreciated 4 months ago, created a post with more than 5 votes. For A: ICGC Variant Calling Pipelines
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: ICGC Variant Calling Pipelines
Student 6 months ago, asked a question with at least 3 up-votes. For Rna-Seq Data Normalization With Spike-In Using Deseq
Popular Question 9 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Teacher 9 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 10 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 11 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Scholar 11 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Scholar 12 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training

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