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• ScatterPlot with CummeRbund
  Hello, I am new to bioinformatics and I am trying to get a scatterplot for my FPKM values, which ...
• Add gene names for significant genes in volcano plot (CummeRbund)
  Hi all, I generated a volcano plot with CummeRbund. Now I want to label the significant genes wi...
• Why is the significance threshold on my cummeRbund volcano plot so high?
  Hi, I recently used the Tuxedo package to analyze RNA-seq data of four conditions each with four...
• how to get R squared value in scatter plot in cummeRbund
  Dear all i need to get R squared value in scatter plot in cummeRbund? how can i get that thanks
• pulling out subset in cummeRbund
  Hello Maestros I found this wonderful intact and working script. gene_diff_data  <- diffData...
• How to make a Scatterplot and a DE gene list from ballgown results?
  Hi and thanks for reading. I have the ballgown element with e.ctab, t.ctab, i.ctab, e2t.ctab, i2...
• CummeRbund: I can't create a dispersion plot - help please?
  Hi all, I am now somewhat familiar with cummeRbund and have all my plots already except for one:...
• cummeRbund grouping by TSS / CDS / Isoforms
  I am working on RNA-seq data with `cufflinks`. I now use `cummeRbund` to analyze my results. `cu...
• WGCNA summary output of network analysis results Probe ID's not working
  After the Intramodular analysis: identifying genes with high GS and MM you do summary output of n...
• Error With Cummerbund: "Could Not Find Function Theme" When Using The Fpkmscvplot Function
  I am getting the following error when i try to use csBoxPlot with cummeRbund: Error in .local(obj...
• How do I change the plot range in dispersionPlot() cummeRbund?
  Hello, I would like to be able to adjust the plot range in of dispersionPlot() in cummeRbund. T...
• Plot table with all replicates in cuffdiff output with cummeRbund
  Hi Can someone help to do the following from the *cummeRbund* package: I only want to plot a si...
• PCA scatterplot with different shapes for different clusters
  This might be a stupid question but if I've already done PCA on the genes from my data (genes as ...
• Scatterplots In R
  I would like to compare two datasets of the same length using scatterplots and then colour the di...
• Scatterplots Showing Correlation Between Gene Pairs
  I have two dataframes x<-data.frame(matrix(rnorm(1000), nrow=1000, ncol=10)) y<-data.fra...
• Does it have something wrong with my Linkage Disequilibrium scatterplot?
  Hi everyone! I'm doing a LD decay plot with data obtained from plink: "plink --bfile mydata --r2...
• How to highlight single gene in volcano plot?
  Hi all, I am in the process of creating a volcano plot from my cuffdiff data. I am using cummeRb...
• How to plot MA plot and volcano plot by using cummeRbund
  Hello every one I need one help. I have xlsx file for my differential expressed gene obtained fr...
• cummerbund cuffset filtering to subset or making a significance matrix from a cuffgeneset
  Hi,   I'm working with a data set that is missing a lot of data due to quality issues. Therefor...
• Scatter plot by cummeRbund
  Hello Everyone I am using cummeRbund package to create scatter plot. I need help to guide me ho...
• Rna -Seq cummeRbund plot issues
  I'm using the tuxedo protocol for RNA-Seq data analysis the analysis is complete but it seems the...
• When I use the function fpkmSCVPlot via cummeRbund, I get one of the lines is horizontal
  When I analysis the differentially expressed gene , I used cummeRbund. I want to see the CV2 via...