User: vchris_ngs

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vchris_ngs4.4k
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Seattle,WA, USA
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https://github.com/vd4...
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@vchris21
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1 day, 2 hours ago
Joined:
4 years, 8 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. Currently working in industry in Omics Drug Discovery.

Posts by vchris_ngs

<prev • 920 results • page 1 of 92 • next >
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Comment: C: extract TCGA data
... Right, my apologies, I should have clarified it better. Mostly the legendary data with RSEM while one can also access STAR aligned data and retrieve counts via HT-Seq and normalized data as well. But to access BAMs (qualifies for raw data since you can go back to prepared the fastq files from them o ...
written 8 days ago by vchris_ngs4.4k
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Comment: C: extract TCGA data
... Here you go [TCGA Assembler][1] is another one apart from TCGAbiolinks and recount. Just remember all these will only provide you with matrix of count data or FPKM/TPM . This means they are quantified with RSEM. You cannot obtain raw data unless you specifically apply for GDC and ICGC approval and g ...
written 8 days ago by vchris_ngs4.4k
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Answer: A: cancer immune subtypes based RNAseq data
... Well adding up to what Kevin has said, if you are new, learn and unlearn to get comfortable. I would not make much of a details, just a bit of cue that should be good enough for your starting point. Try to frame your query as to why you want to use the subtypes and what you intend to address with th ...
written 9 days ago by vchris_ngs4.4k
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Comment: C: Enrichpathway In ReactomePA.
... Have you followed the [vignette][1] properly? There is the hypergeometric model building for total number of genes and `readable=T` parameter library(ReactomePA) data(geneList) de <- names(geneList)[abs(geneList) > 1.5] head(de) x <- enrichPathway(gene=de,pvalueCutoff= ...
written 12 days ago by vchris_ngs4.4k
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Comment: C: CNV detection using BAM file
... as Eric said, you already have your answer. Now coming to more specific. I suppose you are referring to Control-FREEC and not just FREEC. Try to get hold of the most updated one and not the old one. Valentina Boeva maintains the doc pretty well and all the informations are pretty good there. You you ...
written 4 weeks ago by vchris_ngs4.4k
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Comment: C: PCA on sample GO terms
... This seems to be so cool! Thanks a lot for the link ...
written 4 weeks ago by vchris_ngs4.4k
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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 8 weeks ago by vchris_ngs4.4k
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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 12 weeks ago by vchris_ngs4.4k
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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 12 weeks ago by vchris_ngs4.4k
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Comment: C: Difference between tSNE and PCA analysis
... updated. Thanks for pointing it out. ...
written 12 weeks ago by vchris_ngs4.4k

Latest awards to vchris_ngs

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

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