User: researcher

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researcher0
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Posts by researcher

<prev • 18 results • page 1 of 2 • next >
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Comment: C: How can we increase the width of the correlation plot generated by DiffBind
... Hi [Rory][1], sorry I didn't saw your response earlier. Actually, I have 150 samples and want to display all their names in the correlation matrix, but with default settings it is only showing names for 35 samples because of the plot size. How can I resize the plot dimensions so that it will have al ...
written 5 days ago by researcher0
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Comment: C: How to control the text size for colAttributes in the annotation bar for dbaplot
... Kindly someone help, I am really stuck with this. ...
written 5 days ago by researcher0
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How to control the text size for colAttributes in the annotation bar for dbaplot() or dba.plotHeatmap()
... Hi [Rory][1], I am unable to control the text size for colAttributes in the annotation bar for dbaplot() or dba.plotHeatmap(). Can you or anyone please guide how should I do the same. Ill really appreciate your help. Thanks [1]: https://support.bioconductor.org/u/5741/ ...
diffbind dbaplot() dba.plotheatmap() written 6 days ago by researcher0 • updated 5 days ago by James W. MacDonald52k
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Comment: C: a newbie question on ConsensusClusterPlus
... Hi [niki][1], by any chance did you get the answer you were looking for? I am also using ConsensusClusterPlus to know the cluster of my data and was wondering how can I add annotation bar with the samples participants for each cluster. I'll really appreciate any help. [1]: https://support.biocon ...
written 23 days ago by researcher0
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How to change the text size for the names of ColAttributes
... I am using the following command: ``` > plot(DBdata,cexRow=2,cexCol=2,dendrogram='none',lhei = c(0.5,6),lwid = c(0.5,4), ColAttributes=c(DBA_TREATMENT,DBA_CONDITION),key=F, colSideCols=list(c("lightpink","skyblue"),c("chocolate","darkgrey","darkorchid4"))) ``` but unable to control the font siz ...
chipseq diffbind colattributes cex written 26 days ago by researcher0
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Why is the rGREAT's available ontology with category = "Pathway Data" not workin?
... I am using rGREAT to annotate my Chip Seq peaks but suddenly the "availableOntologies(job)" has changed to: [1] "GO Molecular Function" "GO Biological Process" [3] "GO Cellular Component" "Mouse Phenotype" [5] "Mouse Phenotype Single KO" "Human Phenotype" [7] "Ensembl ...
rgreat pathway analisis pathway data getenrichmenttables() availableontologies(job) written 3 months ago by researcher0 • updated 3 months ago by Zuguang Gu180
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
... I am using ChIPseeker to annotate my differential peaks but getting an error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’ I don't have any clue to solve this error. Any suggestion is highly appreciated. ...
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How to find sites with H3K27me3 loss?
... Hi All, I have Chip-Seq data for histone marks (H3K27me3, H3K27ac, H3K4me1 and H3K4me3) for 2 different cancer subtypes which differ in their aggressiveness. I am interested to see if there is any association between the tumor aggressiveness and H3K27me3 loss. I have used Diffbind to call different ...
diffbind macs histone h3k27me3 chip seq written 3 months ago by researcher0
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Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap?
... Hi, Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap? As I have two attributes in my data `DBA_CONDITION`, `DBA_FACTOR` but want to name "Factors" as "Histone Mark" in the figure generated by `plot()` or `dba.plotHeatmap()`. Is it possible to do so? Thanks. ...
diffbind plot dba.plotheatmap plotheatmap written 3 months ago by researcher0 • updated 3 months ago by Rory Stark3.0k
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Comment: C: Can we control colors for two different colAtributes
... Hi **@Rory**, thank you so much for your great help. Does the **colSideCols** also make sure that there should not be an overlap of colors between DBA_TISSUE and DBA_CONDITION? In my additional question, I want to ask how can we add the definition of each color in the legend to show which color r ...
written 3 months ago by researcher0

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