User: vchris_ngs

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vchris_ngs4.2k
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Milan, Italy
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@vchris21
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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 • 897 results • page 1 of 90 • next >
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Comment: C: Salmon Pvalue/FDR results
... salmon does not give such values, as far as I know, you must be plugging in the output of salmon into some DE tool and performing differential expression analysis which gives you logFC for the condition you are testing, and the rest metrics. ...
written 4 hours ago by vchris_ngs4.2k
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Comment: C: Pathway Annotation for variants Exome Data
... This [link][1] should suffice provided your question of interest as of now is pathway analysis from vcf file. I still do not really approve of the pathway analysis from exome data but that link has several inputs as to how to formulate the query as well if it at this point your goal is a bit blurry ...
written 6 hours ago by vchris_ngs4.2k
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Comment: C: heatmap 2 error
... you are plotting rownames against one column so this is not a heatmap rather just a plot of points corresponding to your miRNA id's. So if you want to plot a heatmap either you should make a matrix or dataframe in R for the ID that you are interested, pull the corresponding normalized expression val ...
written 8 hours ago by vchris_ngs4.2k
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Comment: C: sleuth vs deseq2
... I second that what Kevin is saying, however I would like to highlight the paper that should give you an idea of this as well since we performed this test as well. Take a look at [rnaonthebench][1] [1]: https://www.ncbi.nlm.nih.gov/pubmed/27190234 ...
written 8 hours ago by vchris_ngs4.2k
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Comment: C: Using of TPM for miRNA sequencing
... Don't think OP was the gene.length vector so I proposed as it is published on DE analysis on conditions without replicate. However, I still have doubts about it as well. ...
written 10 hours ago by vchris_ngs4.2k
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Comment: C: Using of TPM for miRNA sequencing
... you are missing the point, please read the manuals of GFOLD, the link I posted, it is your work to understand how and why you need to use tools. The link I have given for GFOLD explicitly comes with a tutorial how to use from sam files count data and use GFOLD for DE analysis without replicates. Fo ...
written 10 hours ago by vchris_ngs4.2k
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Comment: C: Using of TPM for miRNA sequencing
... I would second that and also mentioned but there is only one tool which is GFOLD doing such ranking stuff based DE from 1 vs 1 without replicate. Although they should be only used for exploratory. However, the OP seems to have no way to to get replicates so even for exploratory GFOLD can be used. DE ...
written 10 hours ago by vchris_ngs4.2k
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Comment: C: Using of TPM for miRNA sequencing
... Do you have bam file? you can use **featurecounts** of **HT-Seq** to pull the count data from your bam file. I have never used miRDeep2 so cannot tell you about it. What I understand from seq(norm) as you state is probably normalized by library size produced by mirDeep2. You need to check that in th ...
written 11 hours ago by vchris_ngs4.2k
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Comment: C: Using of TPM for miRNA sequencing
... So DESeq2/edgeR and limma works on count data and not TPM for any of the statistics that will build the model for DE analysis. So do not use TPM. Having said that it does not work for one sample per condition for an estimation of DESeq2. The have always maintained to not trust those answers. TPM is ...
written 12 hours ago by vchris_ngs4.2k
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Comment: C: Semantic Similarity selection in REVIGO: which is better? many clusters or few?
... In that case, you will not need semantic similarity. Even other plotting techniques can just reveal that. I would rather follow what Jean is proposing. There is also cluterProfiler for showing enrichment patterns of GO terms. So right now it is a matter of representation for you as far as I understa ...
written 1 day ago by vchris_ngs4.2k

Latest awards to vchris_ngs

Popular Question 7 days ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Teacher 28 days 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 5 weeks ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 10 weeks ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Scholar 10 weeks ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Scholar 3 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 4 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
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
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
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
Scholar 5 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Teacher 6 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 6 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 Ipa With My Gene List
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 Ipa With My Gene List

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