User: researcher

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researcher0
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Posts by researcher

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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 4 weeks ago by researcher0 • updated 28 days ago by Zuguang Gu170
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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 4 weeks 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 7 weeks ago by researcher0 • updated 6 weeks ago by Rory Stark2.8k
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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 7 weeks ago by researcher0
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Can we control colors for two different colAtributes
... How can I control colors for different colAttributes: one as Factor and other is Condition. Can I use different colors for these two cola attributes? Additionally, How can I have the color annotation for each factor and condition. Kindly help. Thanks! ...
diffbind plot plotheatmap written 7 weeks ago by researcher0 • updated 7 weeks ago by Rory Stark2.8k
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Comment: C: How can I remove the row and column labels/names in the plot() or dba.plotHeatma
... Thanks**@Rory** for answering, it really helped. I have another question how can I control colors for colAttributes as I have one as Factor and other as Condition. Can I use different colors for these two? Additionally, How can I have the color annotation for each factor and condition. Kindly help. ...
written 7 weeks ago by researcher0
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Comment: C: How can I remove the row and column labels/names in the plot() or dba.plotHeatma
... Dear Ramrs, I have made the suggested changes to my post. DiffBind do have dba.plotHeatmap() or just plot() to plot correlation matrix which uses heatmap.3 in background as mentioned in the source code [core.R][1] I hope this will be helpful in seeking your help. **@Rory Stark** , can you please ...
written 7 weeks ago by researcher0
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How can I remove the row and column labels/names in the plot() or dba.plotHeatmap() while plotting correlation matrix using diffbind?
... Hi I am using DiffBind's dba.plotHeatmap() or just plot() to plot a correlation matrix between the peak calls. For my correlation matrix I don't want to have the axis labels and thus used the given command plot(DBdata,labRow = NULL, labCol = NULL) but getting the following error: Error ...
diffbind plot heatmap.3 written 7 weeks ago by researcher0 • updated 7 weeks ago by Rory Stark2.8k
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How can we increase the width of the correlation plot generated by DiffBind
... In order to accommodate the whole list of samples on the plot, how can I increase the width of the correlation plot generated by DiffBind ...
diffbind plot(dbdata) written 12 weeks ago by researcher0 • updated 7 weeks ago by Rory Stark2.8k

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