User: Assa Yeroslaviz

gravatar for Assa Yeroslaviz
Assa Yeroslaviz1.3k
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Munich, Germany
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11 years, 2 months ago
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Posts by Assa Yeroslaviz

<prev • 231 results • page 1 of 24 • next >
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Comment: C: biomaRt error when connecting to host
... thanks, this works ...
written 17 days ago by Assa Yeroslaviz1.3k
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biomaRt error when connecting to host
... Hi, I'm trying to connect to biomaRt, but keep getting an error message: Entity 'copy' not defined Error: 1: Entity 'copy' not defined This happen with several different hosts, so I don't think it is a host problem, but who knows... ensembl = useMart( "ensembl", dataset = "scerevisiae_gene_ens ...
biomart connection host written 17 days ago by Assa Yeroslaviz1.3k • updated 17 days ago by Mike Smith1.7k
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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 6 weeks ago by Assa Yeroslaviz1.3k • updated 6 weeks 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 8 weeks 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 8 weeks 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 9 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 9 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 9 weeks ago by Assa Yeroslaviz1.3k • updated 9 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 9 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 9 weeks ago by Assa Yeroslaviz1.3k

Latest awards to Assa Yeroslaviz

Appreciated 16 days ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Popular Question 27 days ago, created a question with more than 1,000 views. For extract intensity values from AffyBatch
Popular Question 11 weeks ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 12 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
Appreciated 12 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Supporter 13 months ago, voted at least 25 times.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Popular Question 18 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Scholar 21 months ago, created an answer that has been accepted. For A: could not find symbol "keepNA" in environment of the generic function
Centurion 2.8 years ago, created 100 posts.

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