User: arta

gravatar for arta
arta180
Reputation:
180
Status:
Trusted
Location:
Sweden
Website:
https://github.com/Tan...
Last seen:
19 hours ago
Joined:
3 years, 2 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 • 42 results • page 1 of 5 • next >
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Answer: A: Database of phosphatase targets
... Did you look [phosphatome][1] ? [1]: http://phosphatome.net/2.0/database/ ...
written 1 day ago by arta180
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Comment: C: Which aligment tool is best for eukaryotic transcriptome?
... [STAR][1] is a good starter. [1]: https://academic.oup.com/bioinformatics/article/29/1/15/272537 ...
written 7 days ago by arta180
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Answer: A: DAVID: p-value and Benjamini correction interpretation
... Benjamini correction is your false discovery rate and it is your adjusted p-value. So you should forget about your p-value after correction. So your test is significant if your adjusted p-value is smaller than criteria (such as 0.05 or 0.01). If you want to more about multiple testing, you can check ...
written 7 days ago by arta180
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Comment: C: Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
... I agree with Smith, by combining them you have ability to decrease the noise. ...
written 8 days ago by arta180
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Answer: A: nearby genes expression
... dds <- DESeq(dds) res <- results(dds) res is the data frame where you can find log2FC in second column `res[,2]` and rownames are genes. dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ co ...
written 12 days ago by arta180
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Comment: C: how to select genes after obtaining read counts
... Yes, you should filter out zero counts, and also low-expressed genes which might be observed due to noise. You can calculate FPKM or TPM [Click here for simple explanation][1] for each gene and plot the distribution and decide an arbitrary cut-off. If the distribution follows a normal distribution, ...
written 20 days ago by arta180
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Answer: A: stringtie and alternative splicing
... You can use [DEXSeq][1] from same guy (Simon Anders) to compare differential exon usage. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf ...
written 21 days ago by arta180
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Comment: C: Statistical test for enrichment of a list of pathways after clustering them
... You should change the type of the post. People assume you have created a tool once they read your post title. Please convert "tool" into "Question". ...
written 22 days ago by arta180
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Answer: A: Statistical test for enrichment of a list of pathways after clustering them
... You can apply hypergeometric test for the significantly enriched pathways. There is already built-in [package][1] in R. I assume you will run around 80 test (4 clusters * ~20 KEGG pathways.) I would have corrected p-values. You can apply [p.adjust][2] function in R. Beside hypergeometric test, I wo ...
written 22 days ago by arta180
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Answer: A: Add annotation color bar to ggplot or ggvis barplot
... You can use [aheatmap][1] package. [1]: http://nmf.r-forge.r-project.org/aheatmap.html ...
written 4 weeks ago by arta180

Latest awards to arta

Commentator 7 days ago, created a comment with at least 3 up-votes. For C: Which aligment tool is best for eukaryotic transcriptome?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Scholar 6 weeks ago, created an answer that has been accepted. For A: microarray data analysis
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: microarray data analysis
Autobiographer 7 weeks ago, has more than 80 characters in the information field of the user's profile.
Popular Question 2.5 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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