User: arta

gravatar for arta
arta580
Reputation:
580
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Location:
Sweden
Website:
https://github.com/Tan...
Last seen:
5 days, 20 hours ago
Joined:
5 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 • 101 results • page 1 of 11 • next >
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Job: PhD position in Edinburg University & Karolinska Institute - Taming the Hippo in Cancer through Proteogenomics-
... You can find all related information [here][1]. [1]: https://www.ed.ac.uk/usher/precision-medicine/project-opportunities/20-21-projects/taming-the-hippo-in-mesothelioma-through-proteogen ...
genomics proteomics job phd position transcriptomics written 4 months ago by arta580
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Comment: C: Journals for rapid publication in computational biology
... Did you check [f1000research][1]? They are really fast, however, i am not sure whether or not they accept review and their impact factor is around 1. [1]: https://f1000research.com/ ...
written 5 months ago by arta580
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Comment: C: Pheatmap X-axis on Top
... Did you check [Complexheatmap][1] which provides large number of customized options? [1]: https://jokergoo.github.io/ComplexHeatmap-reference/book/ ...
written 5 months ago by arta580
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Comment: C: Selecting specific rows in R
... I did not say this is the best solution. This is the another way of solving the current solution. Imagine you want to keep just rows with "X", you can easily modify the code and keep those rows. ...
written 6 months ago by arta580
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Comment: C: Selecting specific rows in R
... The other solution is; ## example data: df1 <- data.frame(X2=c("X",1,2,"X"),X3=c("X",3,4,"X")) ## Delete "X" in each column separately df1.cleaned <- df1[df1$X2 != "X" & df1$X3 != "X" ,] ...
written 6 months ago by arta580
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Answer: A: Learn python programming
... To learn programming you have to keep coding. There is really nice platform called [Rosalind][1]. It is about learning bioinformatics as well as improving coding skills through solving real bioinformatics problems. It is up to you which programming language you use. I would strongly recommend for yo ...
written 7 months ago by arta580
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Comment: C: How to reproduce MATLAB tsne('algorithm', 'exact') result in R?
... t-SNE (t-Distributed **Stochastic** Neighbor Embedding) starts with random initialization that is why each time when you run the algorithm, you get different results (not exactly same, slightly different). In order to reproduce the results in R, you can use `set.seed(x)` where x is numeric value. I ...
written 22 months ago by arta580
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Comment: C: Do gene expression microarrays cover all genes in the transcriptome?
... > Does that mean that microarrays are limited by genes that are known? Yes. > Do they do a good job of probing for all of these known genes? Yes, they design probe for all known genes. But there are limitation of detection as i said before. You can read [that paper][1] where they compare m ...
written 23 months ago by arta580
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Comment: C: Do gene expression microarrays cover all genes in the transcriptome?
... If you aim to detect something new, you can not do that using microarray since it is array (probe) based technology. Even if, you know the sequence and design a probe to capture the sequence, it is not guarantee that you will detect it due to very low and high expression of the sequence. Microarray ...
written 23 months ago by arta580
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Comment: C: how to increase the size of legend in pheatmap
... To continue with @cpad0112's answer, you can try; pheatmap(, cellwidth=x, cellheight=y) where x and y values you can play around to find the best size. ...
written 23 months ago by arta580

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Centurion 4 months ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For How to find genes that are involved in particular pathway ?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to find genes that are involved in particular pathway ?
Popular Question 16 months ago, created a question with more than 1,000 views. For How to find genes that are involved in particular pathway ?
Popular Question 16 months ago, created a question with more than 1,000 views. For Postdoc position in Bioinformatics at Karolinska Institute (Stockholm)
Popular Question 16 months ago, created a question with more than 1,000 views. For How to find genes that are involved in particular pathway ?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
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Scholar 2.4 years ago, created an answer that has been accepted. For A: DAVID: p-value and Benjamini correction interpretation
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Scholar 2.6 years ago, created an answer that has been accepted. For A: microarray data analysis
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