User: Assa Yeroslaviz

gravatar for Assa Yeroslaviz
Assa Yeroslaviz1.3k
Reputation:
1,290
Status:
Trusted
Location:
Munich, Germany
Last seen:
4 weeks ago
Joined:
11 years, 4 months ago
Email:
f*****@gmail.com

Posts by Assa Yeroslaviz

<prev • 233 results • page 1 of 24 • next >
0
votes
0
answers
93
views
0
answers
'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 7 weeks ago by Assa Yeroslaviz1.3k
0
votes
0
answers
76
views
0
answers
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 8 weeks ago by Assa Yeroslaviz1.3k
0
votes
1
answers
286
views
1
answers
Comment: C: biomaRt error when connecting to host
... thanks, this works ...
written 11 weeks ago by Assa Yeroslaviz1.3k
7
votes
1
answer
286
views
1
answer
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 11 weeks ago by Assa Yeroslaviz1.3k • updated 11 weeks ago by Mike Smith1.8k
4
votes
3
answers
191
views
3
answers
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 3 months ago by Assa Yeroslaviz1.3k • updated 3 months ago by Vladimir Kiselev100
0
votes
1
answers
160
views
1
answers
Comment: C: R-3.2.3 install package DESeq2 get wrong
... or maybe update your R version ...
written 3 months ago by Assa Yeroslaviz1.3k
0
votes
1
answers
160
views
1
answers
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 3 months ago by Assa Yeroslaviz1.3k
0
votes
1
answers
155
views
1
answers
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 months ago by Assa Yeroslaviz1.3k
0
votes
1
answers
155
views
1
answers
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 months ago by Assa Yeroslaviz1.3k
0
votes
1
answer
155
views
1
answer
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 months ago by Assa Yeroslaviz1.3k • updated 4 months ago by mat.lesche10

Latest awards to Assa Yeroslaviz

Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Popular Question 12 weeks ago, created a question with more than 1,000 views. For extract intensity values from AffyBatch
Popular Question 4 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 14 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 14 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 14 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
Appreciated 14 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Supporter 15 months ago, voted at least 25 times.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Popular Question 20 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Scholar 24 months ago, created an answer that has been accepted. For A: could not find symbol "keepNA" in environment of the generic function
Centurion 3.0 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 167 users visited in the last hour