User: Assa Yeroslaviz

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Assa Yeroslaviz1.3k
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Posts by Assa Yeroslaviz

<prev • 226 results • page 1 of 23 • next >
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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 2 days 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 6 days 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 ...
differential exon usage dexseq written 6 days ago by Assa Yeroslaviz1.3k • updated 6 days 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 7 days 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 ...
junctionseq reference relevel written 7 days 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 7 days 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 7 days ago by Assa Yeroslaviz1.3k
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sc3_prepare function error
... Hi, I am trying to follow the workflow from the hemberg lab about single-cell analysis. There is though a conflict in the versions. I try to run the SC3 package. There is a function here called sc3_prepare, but under my R environment it doesn't seem to exist. I keep getting the error message (run ...
single cell sc3 single-cell scater written 7 days ago by Assa Yeroslaviz1.3k • updated 7 days ago by Vladimir Kiselev40
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JunctionSeq on multiple conditions
... Hi,  I am testing the JunctionSeq and QoRTs package via the example Walkthrough, but with my data. If I understood the protocol correctly, it supposes to be possible to analyse multiple conditions with one command.  I my case I have four different conditions called ES, EB1-EB3. when running the r ...
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IRanges object from count matrix
... Hi, is there a way to automatically convert the featureCounts result matrix into a GRanges (IRanges) object? by feeding it into GRanges? I ran featureCounts for the data set and have this matrix (first 5 columns):               Chr      Start        End  Strand Length ENSMUSG00000102693    1     ...
counts iranges genomicranges rnaseq featurecounts written 9 days ago by Assa Yeroslaviz1.3k • updated 8 days ago by Hervé Pagès ♦♦ 12k

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Popular Question 17 days ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
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Popular Question 10 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
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Popular Question 16 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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