User: Assa Yeroslaviz

gravatar for Assa Yeroslaviz
Assa Yeroslaviz1.3k
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Munich, Germany
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11 years, 6 months ago
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Posts by Assa Yeroslaviz

<prev • 235 results • page 1 of 24 • next >
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Comment: C: (Big)wig file of complete chromosome
... Thanks Michael for the neat solution. it is still not what i need though. The coverage function summarize the similar values into one row like that: GRanges object with 5793227 ranges and 1 metadata column: seqnames ranges strand | score <Rle> < ...
written 9 days ago by Assa Yeroslaviz1.3k
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(Big)wig file of complete chromosome
... Hi,   I have a list of bigwig files from different data sets. We would like to create a table of all the genomic positions per chromosome to be able to compare the samples with each other.  As the peaks found in each samples are at different chromosomal positions, I would like to complete each ch ...
rtracklayer granges grangeslist bigwig import written 15 days ago by Assa Yeroslaviz1.3k • updated 15 days ago by Michael Lawrence9.4k
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'memory not mapped' error when running monocole
... Hi, when trying to analyse time-sereis analysis of single-cells RNASeq with monocole, my R session crashes, when I try to get the structure of my CellDataSet object.  This is the script I am using ( it is a minimal example I created for the reproduction of the error message): library(monocle) li ...
monocole memory celldataset written 3 months ago by Assa Yeroslaviz1.3k
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Rstudio crashes when running monocole
... Hi, i am trying to run the monocole package on my macBook, but when running the command  CellData <- monocle::newCellDataSet(ddata, phenoData = pdata, featureData = fdata) Rstudio just crashes without any warnings at all.  I have read that monocole doesn't work with too many genes. the d obj ...
rstudio single-cell monocole written 3 months ago by Assa Yeroslaviz1.3k
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Comment: C: biomaRt error when connecting to host
... thanks, this works ...
written 4 months 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 4 months ago by Assa Yeroslaviz1.3k • updated 4 months ago by Mike Smith1.9k
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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 5 months ago by Assa Yeroslaviz1.3k • updated 5 months ago by Vladimir Kiselev100
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Comment: C: R-3.2.3 install package DESeq2 get wrong
... or maybe update your R version ...
written 5 months 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 5 months 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 5 months ago by Assa Yeroslaviz1.3k

Latest awards to Assa Yeroslaviz

Appreciated 4 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Popular Question 4 months ago, created a question with more than 1,000 views. For extract intensity values from AffyBatch
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 15 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 15 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
Appreciated 15 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Supporter 17 months ago, voted at least 25 times.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Popular Question 22 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Scholar 2.1 years ago, created an answer that has been accepted. For A: could not find symbol "keepNA" in environment of the generic function
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