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• Request For Showing Output Plots In Galaxy Frame
  Dear Galaxy team, My name is Matthew Iyer and I am a Bioinformatics PhD student at the Universit...
• run.info file and read_groups info file from cuffdiff Galaxy
  Hi, I am trying to make plots by CummeRbund using Cuffdiff outputs I got from Galaxy. However wh...
• 3-D PCA plot
  Hi, does anyone know if Galaxy.org can do principle component analysis? my boss asked for a 3-D ...
• Overlapping axis labels when graphing quality score box plot
  Hello~ Small SOS. I'm trying to graph the quality box plot and the nucleotide distribution chart...
• Circos plot with phage
  Hello guys! I´ve working in phage sequencing and I want to know if there´s a galaxy tool or a se...
• plotProfile/plotHeatmap - How to change the file names?
  I would like to compare H3K4me3 ChIP peaks of several samples at TSS. Therefore, I used "compute...
• Using DiffBind in Galaxy to generate PCAs of ChIP data
  Hi all, I'm trying to use DiffBind in Galaxy to make a PCA or multiple ChIP-seq sets. I have the ...
• RIP-SEQ or RNA-SEQ
  Hello, I am new to galaxy as well as RNA seq analysis. Although, I did not perform RNA seq, I am...
• DiffBind: Generating a PCA in Galaxy
  Hi all, I'm trying to use DiffBind in Galaxy to make a PCA or multiple ChIP-seq sets. I have the ...
• Galaxy cummeRbund fails to identify sample name for X and Y axis for scatter and volcano plot
  Hello, I have cuff diff sqlite db for 2 samples and I wish to visualise the result using galaxy-c...
• significant genes not shown in the scatter and volcano plots
  hello, When i plot the scatter plot and volcano plot for my cuffdiff output using cummeRbund it s...
• Lefse data adjusting to get a meaningful plot result
  Hi all I have a little question that I will try to explain as far as possible. So basically I ha...
• Cummerbund visualization of expression plot
  I am following the NGS101-16 video on Cuffdiff/Cummerbund to learn how to use Cummerbund. For ex...
• Principle Component Analysis input
  I have multiple single-cell RNA-seq samples for which I have a generated a featureCount output fo...
• multiBamSummary in DeepTools_sample order did not match to the entry
  Hi Everyone, I tried to plot the correlation plots using the DeepTools on the web base Galaxy. ...
• How to make negative values positive for t-test
  Hello everyone, I have an microarray data and I want to use volcanoplot (with t-test) in Matlab b...
• data orders in plotcorrelation
  Hi, I am using galaxy-deeptools to analyze my data. But when I used plot correlation to visualize...
• Loading Fasq.Gz Files Using Ftp
  Hi I am NEW to RNA-seq data and galaxy programs. When I try to up-load the RNA-seq data using Fil...
• Plotting Density Of Snps On Chromosomes
  Dear All, I would like to make a graph in which I can compare SNPs of samples for each chromosom...
• Running MACS2 without a control sample
  While going through the [Analysis of Chip-Seq][1] data tutorial, I realized that one of my input ...
• Question Please -Manhattan Plots
  Dear sir, I was looking through your Galaxy Wiki, but could not find an answer to my question. I...
• Give a list of genes and return Transcription starting sites as a bed file
  Dear there: I have a questions that may seems naive to most of you: does anyone know if there is...
• Remove batch effects with galaxy
  Hello, I am having a problem with batch effects on my RNA sequencing data, where I try to determ...