User: arta

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arta410
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410
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Location:
Sweden
Website:
https://github.com/Tan...
Last seen:
13 hours ago
Joined:
3 years, 6 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 • 76 results • page 1 of 8 • next >
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Comment: C: Human genes correlation to Bacterial genes
... You can combine the two data frame using `human.bacteria <- rbind(Human, Bacteria)` than do correlation analysis. ...
written 5 days ago by arta410
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Answer: A: find significant analysis?
... You can use `hypergeometric test` which is similar to fisher test and in the following [link][1] you can find an example about how to do that. [1]: https://stats.stackexchange.com/questions/16247/calculating-the-probability-of-gene-list-overlap-between-an-rna-seq-and-a-chip-c ...
written 6 days ago by arta410
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Comment: C: How to divide a data set into training and testing data set in MATLAB using cros
... Well, technically it should work. Quick and dirty solution can be transposing the data before applying the function or you can check this [link][1] that i have found. [1]: https://www.mathworks.com/matlabcentral/fileexchange/48538-a-matlab-function-for-randomly-partitioning-date-into-training-- ...
written 6 days ago by arta410
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Comment: C: How to divide a data set into training and testing data set in MATLAB using cros
... Have you looked [this][1] ? Apart from that, do you have to use just MATLAB, you can find more help or documentation if you use python or R. [1]: https://www.mathworks.com/help/stats/cvpartition-class.html ...
written 6 days ago by arta410
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Answer: A: Volcano plot help code
... You can check [ggplot2 documentation][1], [ggplot2 tutorial][2], [ggrepel][3]. These are enough to plot what you have asked for. [1]: http://ggplot2.tidyverse.org/reference/ [2]: http://r-statistics.co/Complete-Ggplot2-Tutorial-Part1-With-R-Code.html [3]: https://cran.r-project.org/web/packa ...
written 7 days ago by arta410
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Comment: C: Is there a way to use CNVkit without a reference from normal samples?
... As far as i know, CNV requires reference genome. If you do not have a reference available, you can either build a de novo reference from your reads or find closest species whose reference file is available. ...
written 19 days ago by arta410
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Job: Postdoctoral researcher (Computational Biologist/Bioinformatician) position on Tumor Metabolism (scholarship) in Stockholm
... Dear all, There is an opening position in Karolinska Institute. [Application][1] At the Department of Physiology and Pharmacology we teach and conduct internationally acclaimed, high-quality research in Physiology, Pharmacology, Anesthesiology and Intensive care. We have around 400 employees, 30 ...
proteomics job rna-seq written 20 days ago by arta410
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Answer: A: How to perform gene ontology analysis with list of upregulated and down regulate
... You can use [topGo][1] or [GOstats][2]. Once you get results, you can plot results using [ggplot2][3]. Or if you would like to do pathway enrichments, you can use [Pathview][4]. There are online tools as well such as [Gorilla][5] which outputs as diagrams as well as raw output. [1]: https://ww ...
written 27 days ago by arta410
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Answer: A: Mapping genomic coordinates to protein-relative coordinates
... You are looking for six frame translation and you can use [translate function][1] in R. Here you can find [example][2]. [1]: http://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/Biostrings/html/translate.html [2]: https://rdrr.io/rforge/seqinr/man/translate.html ...
written 4 weeks ago by arta410
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Comment: C: gene network analysis
... Have you tried [WGCNA][1] package from R. You can also read their paper if you would like to gain more theoretical information. [1]: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/ ...
written 5 weeks ago by arta410

Latest awards to arta

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
Scholar 11 weeks ago, created an answer that has been accepted. For A: DAVID: p-value and Benjamini correction interpretation
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Scholar 4 months ago, created an answer that has been accepted. For A: microarray data analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 2.7 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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