User: e.rempel

gravatar for e.rempel
e.rempel430
Reputation:
430
Status:
Trusted
Location:
Germany, Heidelberg, COS
Last seen:
6 hours ago
Joined:
2 years, 5 months ago
Email:
e*******@dkfz-heidelberg.de

Statistician/bioinformatician.

Posts by e.rempel

<prev • 55 results • page 1 of 6 • next >
1
vote
1
answer
125
views
1
answers
Comment: C: topvariance genes from deseq2 output and heatmap
... I will post my comment on the update here: you could try run heatmap.2(mat, ...) directly after mat <- assay(rld)[ topVarGenes, ] mat <- mat - rowMeans(mat) ...
written 23 hours ago by e.rempel430
5
votes
1
answer
125
views
1
answers
Answer: A: topvariance genes from deseq2 output
... HI, this line takes the top 500 genes with the highest variance. Per default, **order** is sorting in increasing order, thus the author of the code uses the minus sign (but she should have used just *order(..., decreasing = T)* ...
written 1 day ago by e.rempel430
2
votes
1
answer
111
views
1
answers
Answer: A: topGO allGenes argument
... Hi you could use: rownames(topTags(tr)@.Data[[1]]) ...
written 1 day ago by e.rempel430
1
vote
3
answers
255
views
3
answers
Comment: C: Filter by Fold change in DESeq2
... Just a comment: in my opinion, the right approach is to run `res <- results(dds, alpha=0.05)` and then filter based on *log2FoldChange* (eventually remove the rows with NAs, which can appear if the number of reads in one condition equals zero). Thus I would assume that 180 genes are what you are ...
written 21 days ago by e.rempel430
1
vote
3
answers
255
views
3
answers
Answer: A: Filter by Fold change in DESeq2
... Hi, you could filter the **res** object directly in R res <- res[res$log2FoldChange >= 1, ] ...
written 22 days ago by e.rempel430
0
votes
5
answers
388
views
5
answers
Comment: C: code for text file parsing
... Could you please explain what > && !a[$0]++ does? ...
written 22 days ago by e.rempel430
0
votes
3
answers
257
views
3
answers
Comment: C: vennDigram for multiple RNA-seq data
... I agree that the interpreting of 5-way Venn Diagram is not easy. ...
written 25 days ago by e.rempel430
0
votes
3
answers
257
views
3
answers
Comment: C: vennDigram for multiple RNA-seq data
... I am not sure whether plotting proportional 5-way Venn Diagram is even (mathematically) possible. You could also try a shiny [app][1] for plotting of Venn Diagrams. [1]: http://jolars.co/eulerr/ ...
written 25 days ago by e.rempel430
0
votes
3
answers
257
views
3
answers
Answer: A: vennDigram for multiple RNA-seq data
... R-package **SystemPiper** offers the possibility to Plot 2-5 way Venn diagrams. E.g. ![VennDiagram][1] The manual is available on [here][2] [1]: http://www.imsbio.co.jp/RGM-files/R_BC/result/systemPipeR/vennPlot.Rd_005_medium.png [2]: http://www.imsbio.co.jp/RGM/R_rdfile?f=systemPipeR/man/v ...
written 25 days ago by e.rempel430
0
votes
3
answers
903
views
3
answers
Comment: C: network with cytoscape
... Looks like someone joined Biostars just to make some advertising. ...
written 25 days ago by e.rempel430

Latest awards to e.rempel

Appreciated 1 day ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 1 day ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Scholar 1 day ago, created an answer that has been accepted. For A: Heatmap.2 giving specific color to a value and start gradient after
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Supporter 29 days ago, voted at least 25 times.
Scholar 29 days ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Scholar 4 weeks ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Scholar 6 weeks ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about
Appreciated 4 months ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 4 months ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1730 users visited in the last hour