Performs differential expression analyses in R between pairs of sample groups using up to 4 methods: DESeq, DESeq2, EdgeR, and upperquartile normalization with ttest. See respective manuals for differences in method. DESeq, DESeq2 and EdgeR use raw counts as input and perform normalization internally. Similarly, upperquartile normalization is performed prior to the ttest. In general, EdgeR and UQnorm discard 0/NA counts, but DESeq does not. The count matrix needed as input can be calculated with HTSeq, STAR, Kallisto, or any other tool for quantifying RNAseq data.
Version  0.4 

Bundle  sequencing 
Categories  DEG Expression smallRNA 
Authors  Katherine Icay (katherine.icay@helsinki.fi), Alejandra Cervera (alejandra.cervera@helsinki.fi) 
Issue tracker  View/Report issues 
Requires  EdgeR (Rbioconductor) ; DESeq (Rbioconductor) ; DESeq2 (Rbioconductor) ; gtools (Rpackage) 
Source files  component.xml DE_options.r 
Usage  Example with default values 
Name  Type  Mandatory  Description 

expr  CSV  Mandatory  Expression matrix of raw counts. It is required that the first column must contain unique miRNA/smallRNA IDs. Column headers should contain all sample names to be evaluated. Recommended: output file of HTSeqExprMatrix . 
treatment  CSV  Mandatory  List file containing the following information: sample names (matching the column headers of the expr matrix) in the first column, and some additional column labelled "Treatment" defining the groups to be analysed. If performing pairwise analysis, an additional column "Sample" must be given. These are casesensitive column names. NOTE: DESeq, DESeq2 will choose to analyze as the reference factor the first "Treatment" given alphabetically. 
Name  Type  Description 

array  Array<CSV>  Array of DEA results. 
diffExpr  Array<BinaryFile>  Array of RData objects obtained as output of DESeq function from DESeq2 package, as output of estimateDispersions function from DESeq package and/or as output of estimateTagwiseDisp function from ergeR package. 
Name  Type  Default  Description 

DE_pairwise  boolean  true  Performs sample pairwise DE analysis. If false , DE is performed between treatment groups without looking for matched sample pairs. 
options  string  "deseq"  Commaseperated list of possible DEAs to perform. Possible options are "deseq", "deseq2", "edgeR" and/or "uqnorm". Options are not casesensitive, but are spellingsensitive. 
pval  float  0.05  Pvalue cutoff for DEAs. 
Test case  Parameters▼  IN expr 
IN treatment 
OUT array 
OUT diffExpr 


case1  properties  expr  treatment  array  diffExpr  
DE_pairwise=false, 

case2_pairwise  properties  expr  treatment  array  diffExpr  
DE_pairwise=true, 