User: arta

gravatar for arta
arta540
Reputation:
540
Status:
Trusted
Location:
Sweden
Website:
https://github.com/Tan...
Last seen:
2 days, 22 hours ago
Joined:
4 years, 10 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 • 95 results • page 1 of 10 • next >
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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 12 months ago by arta540
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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 13 months ago by arta540
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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 13 months ago by arta540
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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 13 months ago by arta540
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Comment: C: Mapping Ensemble IDs to Entrez - Merge data frames
... I have updated the code, i forgot to add the other package. ...
written 13 months ago by arta540
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Answer: A: Mapping Ensemble IDs to Entrez - Merge data frames
... Try this. source("https://bioconductor.org/biocLite.R") biocLite("org.Hs.eg.db") biocLite("clusterProfiler") library(clusterProfiler) library(org.Hs.eg.db) gene.df <- bitr(gene.list, fromType = "ENSEMBL", toType = c( "ENTREZID", "SYMBOL"), ...
written 13 months ago by arta540
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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 14 months ago by arta540
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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 15 months ago by arta540
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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 15 months ago by arta540 • updated 13 months ago by Biostar ♦♦ 20
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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 15 months ago by arta540

Latest awards to arta

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 6 months ago, created a question with more than 1,000 views. For Postdoc position in Bioinformatics at Karolinska Institute (Stockholm)
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 ?
Teacher 13 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 15 months ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
Teacher 19 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 19 months ago, created an answer that has been accepted. For A: DAVID: p-value and Benjamini correction interpretation
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Scholar 21 months ago, created an answer that has been accepted. For A: microarray data analysis
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 4.1 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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