Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Associate.GI /in <list.Csv.DIR> /gi <nt.gi.csv> [/out <out.DIR>]
  Example:      RNA-seq /Associate.GI 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Clustering /in <fq> /kmax <int> [/out <out.Csv>]
  Example:      RNA-seq /Clustering 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Co.Vector /in <co.Csv/DIR> [/min 0.01 /max 0.05 /out <out.csv>]
  Example:      RNA-seq /Co.Vector 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Contacts.Ref /in <in.fasta> /maps <maps.sam> [/out <out.DIR>]
  Example:      RNA-seq /Contacts.Ref 

  Information:  Generates the data input for the DESeq2 R package.
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Data.Frame /in <in.DIR> /ptt <genome.ptt> [/out out.csv]
  Example:      RNA-seq /Data.Frame 

    /in
    Description:  A directory location which it contains the Ht-Seq raw count text files.

    Example:      /in ""

  Information:  Merges the RPKM csv data files.
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /DataFrame.RPKMs /in <in.DIR> [/trim /out <out.csv>]
  Example:      RNA-seq /DataFrame.RPKMs 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /DEGs /in <diff.csv> [/out <degs.csv> /log_fold 2]
  Example:      RNA-seq /DEGs 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /DEGs.UpDown /in <diff.csv> /sample.table <sampleTable.Csv> [/out <outDIR>]
  Example:      RNA-seq /DEGs.UpDown 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /DESeq2 /sample.table <sampleTable.csv> /raw <raw.txt.DIR> /ptt <genome.ptt> [/design <design, default: ~condition>]
  Example:      RNA-seq /DESeq2 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /DOOR.Corrects /DOOR <genome.opr> /pcc <pcc.dat> [/out <out.opr> /pcc-cut <0.45>]
  Example:      RNA-seq /DOOR.Corrects 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Export.Megan.BIOM /in <relative.table.csv> [/out <out.json.biom>]
  Example:      RNA-seq /Export.Megan.BIOM 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Export.SAM.Maps /in <in.sam> [/contigs <NNNN.contig.Csv> /raw <ref.fasta> /out <out.Csv>]
  Example:      RNA-seq /Export.SAM.Maps 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Export.SSU.Refs /in <ssu.fasta> [/out <out.DIR> /no-suffix]
  Example:      RNA-seq /Export.SSU.Refs 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Export.SSU.Refs /in <ssu.fasta.DIR> [/out <out.DIR>]
  Example:      RNA-seq /Export.SSU.Refs.Batch 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Format.GI /in <txt> /gi <regex> /format <gi|{gi}> /out <out.txt>
  Example:      RNA-seq /Format.GI 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /fq2fa /in <fastaq> [/out <fasta>]
  Example:      RNA-seq /fq2fa 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe 
  Example:      RNA-seq /gast 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /gast.stat.names /in <*.names> /gast <gast.out> [/out <out.Csv>]
  Example:      RNA-seq /gast.stat.names 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Group.n /in <dataset.csv> [/locus_map <locus> /out <out.csv>]
  Example:      RNA-seq /Group.n 

  Information:  Count raw reads for DESeq2 analysis.
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Ht-seq /in <in.sam> /gff <genome.gff> [/out <out.txt> /mode <union, intersection_strict, intersection_nonempty; default:intersection_nonempty> /rpkm /feature <CDS>]
  Example:      RNA-seq /HT-seq 

       [/Mode]
    Description:  The value of this parameter specific the counter of the function will be used, the available counter values are: union, intersection_strict and intersection_nonempty

    Example:      /Mode ""

   [/feature]
    Description:  [NOTE: value is case sensitive!!!] Value of the gff features can be one of the: tRNA, CDS, exon, gene, tmRNA, rRNA, region

    Example:      /feature ""

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Imports.gast.Refs.NCBI_nt /in <in.nt> /gi2taxid <dmp/txt/bin> /taxonomy <nodes/names.dmp_DIR> [/out <out.fasta>]
  Example:      RNA-seq /Imports.gast.Refs.NCBI_nt 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /log2.selects /log2 <rpkm.log2.csv> /data <dataset.csv> [/locus_map <locus> /factor 1 /out <out.dataset.csv>]
  Example:      RNA-seq /log2.selects 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /PCC /expr <expr.matrix.csv> [/out <out.dat>]
  Example:      RNA-seq /PCC 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Rank.Statics /in <relative.table.csv> [/out <EXPORT_DIR>]
  Example:      RNA-seq /Rank.Statics 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /RPKM /raw <raw_count.txt> /gff <genome.gff> [/out <expr.out.csv>]
  Example:      RNA-seq /RPKM 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /RPKM.Log2 /in <RPKM.csv> /cond <conditions> [/out <out.csv>]
  Example:      RNA-seq /RPKM.Log2 

    /cond
    Description:  Syntax format as:  <experiment1>/<experiment2>|<experiment3>/<experiment4>|.....

    Example:      /cond "colR1/xcb1|colR2/xcb2"

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /sid.map /gff <genome.gff> /raw <htseq-count.txt> [/out <out.txt>]
  Example:      RNA-seq /sid.map 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /SPCC /expr <expr.matrix.csv> [/out <out.dat>]
  Example:      RNA-seq /SPCC 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Stat.Changes /deseq <deseq.result.csv> /sample <sampletable.csv> [/out <out.csv> /levels <1000> /diff <0.5>]
  Example:      RNA-seq /Stat.Changes 

  Information:  
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /Statics.Labels /in <in.csv> [/label <Label> /name <Name> /value <value> /out <out.csv>]
  Example:      RNA-seq /Statics.Labels 

  Information:  Generates the cytoscape network model from WGCNA analysis.
  Usage:        G:\GCModeller\manual\bin\RNA-seq.exe /WGCNA /data <dataExpr.csv> /anno <annotations.csv> [/out <DIR.Out> /mods <color.list> /from.DESeq /id.map <GeneId>]
  Example:      RNA-seq /WGCNA 

    /data
    Description:  A sets of RNA-seq RPKM expression data sets, the first row in the csv table should be the experiments or conditions, and first column in the table should be the id of the genes and each cell in the table should be the RPKM expression value of each gene in each condition.
                   The data format of the table it would be like:
                   GeneId, condi1, cond12, condi3, ....
                   locus1, x, xx, x,
                   locus2, y, yy, yyy,
                   locus3, ,z, zz, zzz,
                   ......

    xyz Is the RPKM of the genes

    Example:      /data ""

/anno
    Description:  A table of the gene name annotation, the table should be in formats of
    Id, gene_symbol
    locus1, geneName
    locus2, geneName
    ....

    Example:      /anno ""

   [/mods]
    Description:  Each color in this parameter value is stands for a co expression module, and this parameter controls of the module output filtering, using | character as the seperator for each module color.

    Example:      /mods ""

   [/out]
    Description:  Export directory of the WGCNA data, if this parameter value is not presents in the arguments, then the current work directory will be used.

    Example:      /out ""

   [/From.Deseq]
    Description:  Is the /data matrix if comes from the DESeq analysis result output?
                   If is true, then the expression value will be extract from the original matrix file and save a new file named DESeq.dataExpr0.Csv in the out directory,
                   and last using this extracted data as the source of the WGCNA R script.

    Example:      /From.Deseq ""