User: vchris_ngs

gravatar for vchris_ngs
vchris_ngs4.0k
Reputation:
4,020
Status:
Trusted
Location:
Milan, Italy
Website:
https://github.com/vd4...
Twitter:
@vchris21
Last seen:
an hour ago
Joined:
4 years, 1 month ago
Email:
v*******@gmail.com

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 • 871 results • page 1 of 88 • next >
0
votes
1
answer
74
views
1
answers
Comment: C: Conditional modification of counts in the DESeq Data Set
... I think this is very important to not hack the data. Genes or transcripts not having any expression is fine. Also if the library quality is poor you might end up with not having mRNA abundances for few genes. The best is to check the house keeping genes if they are in line or not or you have ERCC sp ...
written 6 hours ago by vchris_ngs4.0k
0
votes
1
answer
66
views
1
answers
Answer: A: How to identify the important SNPs from several GWAS studies
... [This review][1] should be able to give you are starting point. The basic idea in a nutshell is GWAS will give you are lot of SNPs which mostly will be in non-coding regions. Now to understand their functionality and prioritize them you will need to understand their functional impact. You need to m ...
written 6 hours ago by vchris_ngs4.0k
0
votes
0
answers
105
views
0
answers
Comment: C: Any suggestions upon re-quantifying bam files downloaded from EBI-EGA archive wi
... Thats are great observation. Yes I will sort them and see if this works out or not. I was expecting them to be sorted. But yes there are a lot of warnings like this, I just provided top few ones. ...
written 2 days ago by vchris_ngs4.0k
2
votes
0
answers
105
views
0
answers
Any suggestions upon re-quantifying bam files downloaded from EBI-EGA archive with Salmon?
... > Disclaimer: I have emailed their help-desk about this issue but am not very sure if I > will get the exact replies from looking for or something sooner, so I > am seeking for suggestions here. Recently I have got hold of DCC data from EBI EGA archive and decrypted the data of the RNA-Seq ...
bedtools salmon samtools rna-seq written 2 days ago by vchris_ngs4.0k
0
votes
4
answers
162
views
4
answers
Comment: C: next step after differential expression analysis
... TBH, I am happy to help the OP but the OP should also search for similar queries in biostars and google as it will bring up multiple hits in SEO and not make a redundant question. I am pretty sure this question has been asked plenty of times and there are amazing tutorials online as well that gives ...
written 2 days ago by vchris_ngs4.0k
0
votes
4
answers
162
views
4
answers
Comment: C: next step after differential expression analysis
... I would not encourage to use GeneCodis as I see it was last updated in 2011, 6 years in this field totally takes off a tool from the research market. For any Pathway and GO enrichment, updated tools that resource the latest or an update was done in 2016 as of now should be used. ...
written 2 days ago by vchris_ngs4.0k
0
votes
4
answers
162
views
4
answers
Comment: C: next step after differential expression analysis
... You have to read some papers to understand what you have do as q functional analysis post DEGs finding. There are a lot of things you can do depending upon the questions you want to address. Read some functional papers you will get the flavor of also how to represent. For pathway you can look at Enr ...
written 2 days ago by vchris_ngs4.0k
1
vote
1
answer
151
views
1
answers
Comment: C: Copy number variation in normal and cancer tissue
... The one posted in the above answer is one of the most recent paper that you can get your hands on. There is another paper which is using Massively Multiplexed PCR Methodology and then employing NGS for finding CNVs. Take a look [here][1]. This is more reliant on the method. However, with targeted se ...
written 3 days ago by vchris_ngs4.0k
2
votes
1
answer
109
views
1
answers
Comment: C: Is there any way to generate interval list from available exome data?
... you should have an interval list which you can generate as Pierre suggested, however, if you are using Agilent kit when the v4/v5 that were used for the library enrichment for getting the exonic baits should have an internal bed file. This should be provided by the company or should be available onl ...
written 3 days ago by vchris_ngs4.0k
0
votes
0
answers
109
views
0
answers
Comment: C: segFault error in getTCGA : 'memory not mapped'
... probably an issue of some version of a dependency package that was installed in binary version. So do not save the workspace. remove all the installed packages. restart the session or R or R studio whatever you are using, install TCGA2STAT again, load the library and try to run. It should be not a p ...
written 7 days ago by vchris_ngs4.0k

Latest awards to vchris_ngs

Popular Question 6 days ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Scholar 8 days ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 28 days ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Scholar 4 weeks ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 11 weeks ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
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
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
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
Scholar 3 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Teacher 4 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 4 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Popular Question 4 months ago, created a question with more than 1,000 views. For Ipa With My Gene List
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 Ipa With My Gene List
Teacher 7 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 7 months ago, created a question with more than 1,000 views. For Ipa With My Gene List
Popular Question 10 months ago, created a question with more than 1,000 views. For Ipa With My Gene List
Popular Question 10 months ago, created a question with more than 1,000 views. For Ipa With My Gene List
Popular Question 10 months ago, created a question with more than 1,000 views. For Sorting the cbioportal web output of oncoprint based on frequency percentage

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1409 users visited in the last hour