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• How To Run Deseq? Please Help.
  Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differ...
• 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...
• How To Determine Differentially Expressed Genes Using Galaxy?
  Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differ...
• sam to counts in toolbox
  I am trying to run DEseq with my rna seq data.  I am following the tutorial "http://training.bio...
• Lost headers on Deseq analysis
  I performed Deseq analysis on galaxy and after getting the tabular file with the genes and p valu...
• 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...
• Regarding Galaxy Wrappers: "Lumi", "Deseq" "Edger"
  Hi, These are the R libraries. Have anyone written a wrapper for these libraries "lumi", "DESeq"...
• Biological Replicates on galaxy/ DeSeq analysis
  Hi, I am doing RNA seq analysis and I want to preform Deseq. I have 2 replicates for each condit...
• Sub groups within galaxy shed tool conf file
  How do you add subsections to the shed tool conf file so tools can be grouped under each drop-dow...
• DESeq Every Gene Contains at Least One Zero Error
  Have you experienced this error in galaxy?: Fatal error: An undefined error occurred, please...
• DESeq2 Error on Cloudman
  Hi I'm working on Cloudman doing RNASeq transcriptome analysis. I've made BAM file using TopHat2...
• How to feed Deseq in Galaxy with custom count tables?
  Hi, In Galaxy it says Deseq is using count tables for each sample from htseq-count. I want to ...
• Visualizing CuffDiff Data
  Hi,  I've run an RNAseq experiment to look for differentially expressed genes using CuffDiff. I'...
• 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...
• HISAT2 output error
  Hello, We recently ran a set of samples through galaxy from Genewiz. Of our samples, two are not...
• Stringtie tool failed with error "NameError: name 't_id' is not defined"
  Hello I have used the Stringtie tool successfully to produce transcript assemblies and additiona...
• Install Tools From Toolshed
  HI, I am trying to install Deseq from the toolshed. I get the message:Repository installation is ...
• Galaxy - Error
  Dear Malito, I am PhD student and I am working with a bacterial transcriptome. A few days ago, i...
• Using DESeq w/ counts from different RNASeq experiments
  Hello there I have count files from 3 different sequencing experiments on similar samples but wi...
• help with start DESeq
  Hi, I want to analyze my RNA-seq data in DESeq2. I have the following code: library( "GenomicF...
• Table With Gene Count Reads
  Hello Mike, SAM datasets can be used as tabular data with the Text manipulation, Filter and Sort...
• DESeq Duplicated Row Names Error
  Have you experience a similar error like this in Galaxy?: Fatal error: An undefined error oc...