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• How To Determine Differentially Expressed Genes Using Galaxy?
  Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differ...
• DESeq in Galaxy
  Can someone point me if there are sample work flows for running DESeq with in galaxy after runnin...
• input file types to DESeq on the cloud
  Hi there, I've had a go at using the Ratsch lab DESeq tool but it seems to require your input fi...
• R Scripts For Deseq
  Hello, I am planning to put DESeq into galaxy. I am a newcomer for both Galaxy and R. I have alr...
• help with start DESeq
  Hi, I want to analyze my RNA-seq data in DESeq2. I have the following code: library( "GenomicF...
• htseq-count issues with Deseq2
  This is the first time im trying this but I keep running into issues. I'm running the htseq-count...
• HISAT2 output error
  Hello, We recently ran a set of samples through galaxy from Genewiz. Of our samples, two are not...
• Visualizing CuffDiff Data
  Hi,  I've run an RNAseq experiment to look for differentially expressed genes using CuffDiff. I'...
• sam to counts in toolbox
  I am trying to run DEseq with my rna seq data.  I am following the tutorial "http://training.bio...
• Creating StringTie output that meets DESeq expected input content for DE analysis
  Good Morning, Since StringTie can produce output files for differential expression that can be us...
• Table With Gene Count Reads
  Hello Mike, SAM datasets can be used as tabular data with the Text manipulation, Filter and Sort...
• getting old tool on usegalaxy.org
  Is there a way that I can go back to older version of Galaxy in usegalaxy.org? I build one compli...
• No output from Cuffdiff
  Hi, I've been running Cuffdiff on Galaxy today, exactly as I did last week (using the same refer...
• Using DESeq w/ counts from different RNASeq experiments
  Hello there I have count files from 3 different sequencing experiments on similar samples but wi...
• Lost headers on Deseq analysis
  I performed Deseq analysis on galaxy and after getting the tabular file with the genes and p valu...
• Galaxy Ka/Ks?
  Hello. I remember reading that Galaxy can perform Ka/Ks calculations on aligned sequences. I can...