User: Assa Yeroslaviz

gravatar for Assa Yeroslaviz
Assa Yeroslaviz1.3k
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Munich, Germany
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6 days, 12 hours ago
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11 years, 1 month ago
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Posts by Assa Yeroslaviz

<prev • 229 results • page 1 of 23 • next >
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using SC3 and scater for bulk-RNAseq
... Hello I was wondering whether it makes sense (or even possible) to use the SC3-scater packages to analyse bulk-RNA. We have a data set from human cancer with ~350 samples. In those I have three risk groups and multiple abnormalities within, which I would like to use like with scRNA as cell types an ...
scater sc3 scrnaseq written 13 days ago by Assa Yeroslaviz1.3k • updated 13 days ago by Vladimir Kiselev50
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Comment: C: R-3.2.3 install package DESeq2 get wrong
... or maybe update your R version ...
written 22 days ago by Assa Yeroslaviz1.3k
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Answer: A: R-3.2.3 install package DESeq2 get wrong
... use source("https://bioconductor.org/biocLite.R") biocLite("DESeq2") or download it from here to your computer and install it. ...
written 22 days ago by Assa Yeroslaviz1.3k
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Comment: C: dexseq doesn't identify exons as differential
... Hi thanks for the explanation and the link. I think I have understood what the goal of DEXSeq, but than again it still doesn't do what you say, at least not for all the exons. In the gene I have shown above there are almost two separate parts to the gene. (From the biological side, there is an alter ...
written 4 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: dexseq doesn't identify exons as differential
... the link to the images, if needed are added: https://s26.postimg.org/rzjgcfd8p/splicing.png https://s26.postimg.org/6rad8qo5l/counts.png https://s26.postimg.org/5qa4jm761/expression.png   ...
written 4 weeks ago by Assa Yeroslaviz1.3k
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dexseq doesn't identify exons as differential
... hi,  I was wondering how dexseq is calculating the differential exon usage. I am having troubles interpreting the results, which I think are significant, but dexseq does not :-) I have here one of the genes from my run, which looks to me, that it is very much differentially used. the three plots a ...
dexseq differential exon usage written 4 weeks ago by Assa Yeroslaviz1.3k • updated 4 weeks ago by mat.lesche10
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Comment: C: Chemical formula for cacodylate?
... this has nothing to do with this forum. did you even try to google it? ...
written 4 weeks ago by Assa Yeroslaviz1.3k
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Setting relevel with the JunctionSeq package
... Hi, I was wondering if there is a way to set a reference in the function runJunctionSeqAnalysis, like it can be done in DESeq. in the manual it says it will always regards the first factor as  the reference. But what if I want to have the second factor as a reference. Is there  a way to set this i ...
reference relevel junctionseq written 4 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: sc3_prepare function error
... thanks I have updated R to 3.3.2 and bio to 3.4. now it works. I do get a different error message, but this seems to be something else.  when running the jackStraw function it throws back an error -  > d <- jackStraw( + d, + num.replicate = 200, + do.print = FALSE, + num.pc ...
written 5 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: sc3_prepare function error
... I have updated the SC3 package to 1.3.14. Now I get a different error message, which is even before the sc3_prepare error. when running this command  patient.sceset <- sc3(patient.sceset, ks = 2:5, k_estimator = TRUE, biology = TRUE) I get the following error  Setting SC3 parameters... Err ...
written 5 weeks ago by Assa Yeroslaviz1.3k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 11 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Appreciated 11 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
Popular Question 11 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Popular Question 17 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
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