User: vchris_ngs

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vchris_ngs4.3k
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Milan, Italy
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https://github.com/vd4...
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@vchris21
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5 hours ago
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4 years, 6 months ago
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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. 

 

Posts by vchris_ngs

<prev • 914 results • page 1 of 92 • next >
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Comment: C: Gene Prediction Softwares
... So these are Refseq ID. What do you want to do with the annotation and which species they belong to? geneSCG is clustering them based on functional relevance but these are too many ids, probably the entire transcriptome. Tell specifically the aim of the design and what you want to perform. ...
written 1 day ago by vchris_ngs4.3k
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Comment: C: Difference between tSNE and PCA analysis
... I guess you have to check what the OP wrote in comments as biological application. ...
written 27 days ago by vchris_ngs4.3k
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Comment: C: Difference between tSNE and PCA analysis
... Nice one, that is the reason I never used the term clustering ;) ...
written 27 days ago by vchris_ngs4.3k
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Comment: C: Difference between tSNE and PCA analysis
... updated. Thanks for pointing it out. ...
written 27 days ago by vchris_ngs4.3k
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Comment: C: Difference between tSNE and PCA analysis
... It is used for dimensionality reduction and now depending upon variables and your interest of inferencing the applications will be considered. PCA has been a pretty favorite tool till date for RNA-Seq , ChIP-Seq and also WES data, but with incoming scRNASeq and also large scale SNPs data scoring pop ...
written 27 days ago by vchris_ngs4.3k
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Answer: A: Difference between tSNE and PCA analysis
... I can suggest some links that will give you the flavor of both the methods that are used in dimensionality reduction. 1. [Link1][1] 2. [Link2][2] 3. If w.r.t scRNA-Seq check [here][3] 4. For bulk RNASeq check [here][4] 5. If you are a fan of kaggle this [link][5] is pretty fun as well for usag ...
written 27 days ago by vchris_ngs4.3k
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Comment: C: Google announces DeepVariant
... I totally agree how the hoopla over "Google AI solved genomics!" is on. At the end of the day it is a product they are bringing and pretty sure the buzz will be more than what it actually preaches. Having said that, I will feel it is worth taking a look at it as to how germline calls are made and im ...
written 11 weeks ago by vchris_ngs4.3k
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Comment: C: Google announces DeepVariant
... haha, sounds familiar but I was expecting this from Google, finally its out and to be honest seems pretty impressive with Open Source availability as well. ...
written 11 weeks ago by vchris_ngs4.3k
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Comment: C: DESeq2 normalization without the house keeping genes
... I agree to that but OP need to clarify if the QC reports of fastq was problematic or not or let's say the alignment. Problems can be a lot but if the OP is starting with exploratory analysis on counts then filtering is not to be ruled out. Only if it reduces the expression to a lot then it is big re ...
written 11 weeks ago by vchris_ngs4.3k
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Comment: C: DESeq2 normalization without the house keeping genes
... It is a scenario which happens for non-coding RNAs but also true for protein-coding mRNA transcripts as well if the library is not done well or library enrichment is not in accordance with the kind of regions one is looking for. Another problem is are you quantifying across whole genome or only tran ...
written 11 weeks ago by vchris_ngs4.3k

Latest awards to vchris_ngs

Student 28 days ago, asked a question with at least 3 up-votes. For Rna-Seq Data Normalization With Spike-In Using Deseq
Popular Question 3 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
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
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 5 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Scholar 5 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Scholar 6 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
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
Popular Question 8 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Teacher 8 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 8 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
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
Scholar 9 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Popular Question 9 months ago, created a question with more than 1,000 views. For Ipa With My Gene List
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training

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