User: ivivek_ngs

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ivivek_ngs5.0k
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Seattle,WA, USA
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https://github.com/vd4...
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@ivivek87
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16 hours ago
Joined:
7 years, 5 months ago
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v*******@gmail.com

I did my Ph.D. 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 into the field of single-cell which is pretty interesting to me as of now (still working on it as per requirement in the industry).

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. 

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 the industry in Biomarkers & Target Discovery employing Integrative Computational Systems Medicine approach.

Posts by ivivek_ngs

<prev • 976 results • page 1 of 98 • next >
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Comment: C: Databases miRNA sequencing data
... A few things here. AFAIK GTEx does not have microRNA data and also it does not have cancer data. More on data summary and tissue information can be found [here][1]. One can also use [Recount2][2] to access and download GTEx data (although check the version release, as it might not be the latest). ...
written 8 weeks ago by ivivek_ngs5.0k
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Comment: C: How calculate the inflation factor after a linear model run with Limma?
... Hi, if I understand correctly you want to find out the variance inflation factor from this data right? Isn't there a function in limma like the `camera` and `cameraPR` that provides are `data.frame` with all these statistics? It also provides you a column with variance inflation factor (vif). Have y ...
written 8 weeks ago by ivivek_ngs5.0k
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Comment: C: Integrate metabolomic and pathway information
... I have been doing some similar work. Currently, I am using the [MetaboAnalyst][1] for this purpose where I can not only perform KEGG pathway analysis but also separate Metabolite enrichment analysis. There is also the programmatic version available [here][2]. Check it out and try if it works at your ...
written 8 weeks ago by ivivek_ngs5.0k
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Comment: C: RNA-seq batches across different tissues
... Do you know all the factors are causing the batch effect e.g. lane and other lab data? If your PCA is already showing variability due to lane effects and due to other labs, then you can perform the same using the COMBAT or edgeR `removeBatcheffct()` function. SVA is amazing and great when you are un ...
written 8 weeks ago by ivivek_ngs5.0k
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Comment: C: How to call CNV without normal samples
... There is no straightforward way to answer this but often I have seen Panel of Normals (PON) being used for such. Check this [thread][1] from Kevin Blighe. Might be of help. Copy number events can be called from the data but somatic without a reference is always tricky. [1]: https://www.biostars ...
written 8 weeks ago by ivivek_ngs5.0k
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Comment: C: Databases miRNA sequencing data
... Have you tried `TCGABiolinks` where one can download the miRNA expression data for specific cancers. Here is a [link][1] with some `R` code. This used to be one way but I have not tried it recently. The other way I can think of is to search Gene Expression Omnibus using terms like microRNA AND Canc ...
written 8 weeks ago by ivivek_ngs5.0k
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Comment: C: Integrating Mutation, RNAseq and RPPA data toolset
... Well, this is a very different question than what you asked for in this thread. This is a hypothesis that you want to present in a graphical abstract. 1. Have you already used any of the multi-omics integration tools at your end to see if your data already shows a p53 mutation that regula ...
written 10 weeks ago by ivivek_ngs5.0k
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Comment: C: Integrating Mutation, RNAseq and RPPA data toolset
... Depends on what you want to achieve. Do you want to use integration via 1. correlation or probabilistic modeling? 2. Use the unsupervised method (MOFA) or supervised method (mixOmics-DIABLO)? 3. Simple canonical correlational analysis (CCA) using mixOmics and then look up the gene sets between R ...
written 11 weeks ago by ivivek_ngs5.0k
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Comment: C: Producing such a plot in r
... Does not seem like so. The Y-axis here refers to the frequency of gain and deletion %, which in the OP query is the last column ***(Percentage_altered)*** if I understand correctly. ...
written 11 weeks ago by ivivek_ngs5.0k
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Comment: C: Producing such a plot in r
... It seems to me that is a mix of inverted volcano plot and bubble plot. Two links that can help you to achieve the below as per my experience are below: 1.[https://www.r-graph-gallery.com/320-the-basis-of-bubble-plot.html][1] 2.[https://www.bioconductor.org/packages/release/bioc/vignettes/Enhance ...
written 11 weeks ago by ivivek_ngs5.0k

Latest awards to ivivek_ngs

Appreciated 4 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Answer 4 months 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
Popular Question 6 months ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
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
Popular Question 10 months ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
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 17 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 19 months ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
Teacher 19 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 22 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Great Question 2.1 years ago, created a question with more than 5,000 views. For Variant Reduction Using Annovar
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: ICGC Variant Calling Pipelines
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field

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