User: arta

gravatar for arta
arta490
Reputation:
490
Status:
Trusted
Location:
Sweden
Website:
https://github.com/Tan...
Last seen:
2 days, 20 hours ago
Joined:
3 years, 8 months ago
Email:
t***********@ki.se

I am PhD student at Karolinska Institute with a background bioinformatics. I am analyzing the high-throughput datasets (exome & RNA sequencing data, proteomics data) and develop new algorithms to understand the cancer better.

Posts by arta

<prev • 89 results • page 1 of 9 • next >
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Comment: C: Classify benign tumor vs malign tumor
... Well first of all welcome to machine learning field. So for your research, you need to build a model (which can be logistic regression, random forest, support vector machine or naive bayes, etc..) and find the best classifier which separates benign and malign tumor more accurately. Once you build th ...
written 9 days ago by arta490
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Comment: C: Which repository is more appropriate to submit for cancer cell line (bulk) RNA-s
... We will publish it soon. So ENA makes more sense. Thanks. ...
written 5 weeks ago by arta490
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6 follow
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Which repository is more appropriate to submit for cancer cell line (bulk) RNA-seq data ?
... I would like to submit our RNA-seq data (2 cell lines with triplicates) to repository to make it public. I know there are some options such as Sequence Read Archive (SRA) and European Nucleotide Archive. How do you submit your data, i mean how do you decide ? Is there any criteria ? ...
rna-seq written 5 weeks ago by arta490 • updated 5 weeks ago by arup410
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Answer: A: What is gene ontology exactly?
... "Three categories of GO Biological process refers to a biological objective to which the gene or gene product contributes. A process is accomplished via one or more ordered assemblies of molecular functions. Processes often involve a chemical or physical transformation, in the sense that something ...
written 5 weeks ago by arta490
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Comment: C: copy number variation
... Did you see [Copy Number Variation Tools][1] question that was asked before ? [1]: https://www.biostars.org/p/242992/ ...
written 6 weeks ago by arta490
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Comment: C: DAPC different clustering results
... For each run use different set.seed() it could be any integer number. So if you set to 20 you will always get same results if you run same code. Just use different set.seeds. ...
written 9 weeks ago by arta490
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Comment: C: DAPC different clustering results
... How different are the clusters ? Do they fluctuate a lot at each run ? To optimize your clustering, i would run, say 50 times, `find.clusters` function and get the optimal number using your `stat= "BIC"` which is the statistical measure of goodness of fit. And to reproduce your results use `set.se ...
written 9 weeks ago by arta490
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Comment: C: The inconsistency of bulk and single cell RNA-seq results
... Unfortunately, i am not expert in singe-cell rna-seq and can not give you a perfect answer, but in case if you haven't seen these papers before [SCnorm: robust normalization of single-cell RNA-seq data][1] and [Normalizing single-cell RNA sequencing data: challenges and opportunities][2], you could ...
written 10 weeks ago by arta490
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Comment: C: The inconsistency of bulk and single cell RNA-seq results
... The reason of getting low overlap, what i assume, is heterogeneity or simply, the biology. Bulk RNA-seq could mask the variance (hidden biology), within cells. Recently, I have read a ["Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation" ...
written 10 weeks ago by arta490
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Comment: C: "header" function in R
... instead use > res <- read.table("C:/R Database/Volcano/results.txt", header= TRUE) ...
written 11 weeks ago by arta490

Latest awards to arta

Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
Scholar 5 months ago, created an answer that has been accepted. For A: DAVID: p-value and Benjamini correction interpretation
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Scholar 7 months ago, created an answer that has been accepted. For A: microarray data analysis
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to find genes that are involved in particular pathway ?

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