User: Deepak Tanwar

gravatar for Deepak Tanwar
Deepak Tanwar4.1k
Reputation:
4,070
Status:
Trusted
Location:
ETH Zürich, Switzerland
Website:
https://www.linkedin.c...
Twitter:
d_k_tanwar
Last seen:
1 month, 2 weeks ago
Joined:
5 years, 11 months ago
Email:
d*******@hotmail.com

I received my Bachelor in Technology with major in Bioinformatics from Amity University Rajasthan, India in 2014. I did my Bachelor thesis at University of Jena, Germany, where I worked on a Sepsis patient data set and got my thesis published with GRIN publishers. I took my first job as a Visiting Scientist at University of Alabama at Birmingham, USA in 2014. I worked on Cancer patient datasets obtained from TCGA, ICGC and Cosmic consortiums. My findings suggest that mitochondria directed therapies can impact survival of epithelial ovarian cancer patients, which is published in Oncotarget. I have also worked on Proteomes from Pfam and Uniprot databases, aiming to create a N-gram language models of protein domain architecture to investigate evolution and to derive a new method of phylogenetic tree construction. My background and training is in Bioinformatics (Data Science) and am currently pursuing a PhD. at ETH Zürich, Switzerland.

Posts by Deepak Tanwar

<prev • 164 results • page 1 of 17 • next >
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Comment: C: How to perform analysis for repetitive elements in ATAC-Seq data?
... I do not have a sparse matrix for ATAC-Seq data. After filtering out the RE with low counts, I still left with approx. 1.5M RE. I did not filter out reads with MAPQ less than 30. But, for RNA-Seq, one has to allow for multi-mapping. For point number 2 in my question: https://doi.org/10.1186/s13100 ...
written 9 weeks ago by Deepak Tanwar4.1k
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How to perform analysis for repetitive elements in ATAC-Seq data?
... Hello! I have questions about performing repeat-elements (RE) analysis in ATAC-Seq data. So, I have RE information from repeatmasker [RE elements table screenshot](https://ibb.co/NWrtP3Y) Now, I have `bam` files from ATAC-Seq. I think I have 2 approaches to know which repeat-elements have less ...
repeat-elements atac-seq written 9 weeks ago by Deepak Tanwar4.1k
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CNV analysis from WGBS data
... Hello! Which tools can I use for CNV analysis from WGBS data? Can I use tools like CNVkit or CNVnator, followed by [CNVRanger](https://bioconductor.org/packages/release/bioc/vignettes/CNVRanger/inst/doc/CNVRanger.html)? ...
R wgbs cnv written 8 months ago by Deepak Tanwar4.1k • updated 8 months ago by ATpoint40k
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How comparable is MeDIP-Seq with RRBS/WGBS?
... How comparable are MeDIP and RRBS/WGBS data? If I do both MeDIP and RRBS on the same samples, should I expect to obtain similar results? ...
wgbs medip rrbs written 12 months ago by Deepak Tanwar4.1k
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Comment: C: How to create own SRAdb
... Sorry, I updated mine comment! ...
written 16 months ago by Deepak Tanwar4.1k
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Comment: C: How to create own SRAdb
... *The ideal situation would be to pull the data in real time from SRA:* Yes! I was looking for the code which Sean Davis and his team wrote to make this database. But, couldn't find it (that would have been an easy solution)... ...
written 16 months ago by Deepak Tanwar4.1k
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Comment: C: How to create own SRAdb
... As far as I understood, Sean Davis seems to be working on a replacement of SRAdb. As I have already set up the tool to work with SRAdb, I would like to have an updated one. ...
written 16 months ago by Deepak Tanwar4.1k
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Comment: C: How to create own SRAdb
... https://github.com/seandavi/SRAdb/issues/24 ...
written 16 months ago by Deepak Tanwar4.1k
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How to create own SRAdb
... Hello, As SRAdb is outdated, I would like to create my own SRAdb. What is the best way to do that? I am aware of the files I would need to make one: ftp://ftp.ncbi.nlm.nih.gov/sra/reports/ But, I am not an expert in `SQL` and don't know how to deal with `XML` files. ...
geo sra sradb written 16 months ago by Deepak Tanwar4.1k • updated 16 months ago by Sean Davis26k
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How to perform GSEAPreranked analysis in a proper manner?
... Hello! I want to perform GSEA analysis on a list of genes. Out of the following two options, which one should I use and why? 1. List of all genes with their **log-fold-change** values. 2. filtered list of genes with their **log-fold-change** values. Here, the filter could be ***p-value***, ***FDR ...
gsea written 21 months ago by Deepak Tanwar4.1k • updated 21 months ago by mikhael.manurung20

Latest awards to Deepak Tanwar

Great Question 12 weeks ago, created a question with more than 5,000 views. For Bioinformatics courses, workshops or training
Popular Question 5 months ago, created a question with more than 1,000 views. For Graph viewer for Reactome Pathways
Popular Question 5 months ago, created a question with more than 1,000 views. For Graph viewer for Reactome Pathways
Scholar 12 months ago, created an answer that has been accepted. For A: normilization with RMA
Scholar 12 months ago, created an answer that has been accepted. For A: Difficulty installing keggrest and httr in R
Scholar 12 months ago, created an answer that has been accepted. For A: GO term enrichment
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Can someone tell me journal with 1 impactfactor with minimum charge around INR 6
Popular Question 18 months ago, created a question with more than 1,000 views. For Graph viewer for Reactome Pathways
Popular Question 20 months ago, created a question with more than 1,000 views. For Are protein domains indivisible?
Popular Question 20 months ago, created a question with more than 1,000 views. For Graph viewer for Reactome Pathways
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Graph viewer for Reactome Pathways
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Interships in Bioinformatcs
Epic Question 2.1 years ago, created a question with more than 10,000 views. For Bioinformatics courses, workshops or training
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Graph viewer for Reactome Pathways
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Using markdown for two or more programming languages
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Using markdown for two or more programming languages
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Using markdown for two or more programming languages
Great Question 2.9 years ago, created a question with more than 5,000 views. For Bioinformatics courses, workshops or training
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: GO term enrichment
Student 3.3 years ago, asked a question with at least 3 up-votes. For Which is the best smoothing technique for replacing zeros from data?
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: Bioinformatics courses, workshops or training.
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: Can someone tell me journal with 1 impactfactor with minimum charge around INR 6
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: pathway analysis tools and KEGG gene sets from MSigDB
Appreciated 3.6 years ago, created a post with more than 5 votes. For Using markdown for two or more programming languages
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: GO term enrichment

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