1. 1. GCModeller [version 1.0.0.0]
    1. 1.1. Commands
      1. 1.1.0.0.1. Help for command ‘/Associate.GI’:
      2. 1.1.0.0.2. Help for command ‘/Clustering’:
      3. 1.1.0.0.3. Help for command ‘/Co.Vector’:
      4. 1.1.0.0.4. Help for command ‘/Contacts.Ref’:
      5. 1.1.0.0.5. Help for command ‘/Data.Frame’:
    2. 1.1.0.1. Accepted Types
      1. 1.1.0.1.1. /in
      2. 1.1.0.1.2. Help for command ‘/DataFrame.RPKMs’:
      3. 1.1.0.1.3. Help for command ‘/DEGs’:
      4. 1.1.0.1.4. Help for command ‘/DEGs.UpDown’:
      5. 1.1.0.1.5. Help for command ‘/DESeq2’:
      6. 1.1.0.1.6. Help for command ‘/DOOR.Corrects’:
      7. 1.1.0.1.7. Help for command ‘/Export.Megan.BIOM’:
      8. 1.1.0.1.8. Help for command ‘/Export.SAM.Maps’:
      9. 1.1.0.1.9. Help for command ‘/Export.SSU.Refs’:
      10. 1.1.0.1.10. Help for command ‘/Export.SSU.Refs.Batch’:
      11. 1.1.0.1.11. Help for command ‘/Format.GI’:
      12. 1.1.0.1.12. Help for command ‘/fq2fa’:
      13. 1.1.0.1.13. Help for command ‘/gast’:
      14. 1.1.0.1.14. Help for command ‘/gast.stat.names’:
      15. 1.1.0.1.15. Help for command ‘/Group.n’:
      16. 1.1.0.1.16. Help for command ‘/HT-seq’:
    3. 1.1.0.2. Accepted Types
      1. 1.1.0.2.1. /Mode
      2. 1.1.0.2.2. /feature
      3. 1.1.0.2.3. Help for command ‘/Imports.gast.Refs.NCBI_nt’:
      4. 1.1.0.2.4. Help for command ‘/log2.selects’:
      5. 1.1.0.2.5. Help for command ‘/PCC’:
      6. 1.1.0.2.6. Help for command ‘/Rank.Statics’:
      7. 1.1.0.2.7. Help for command ‘/RPKM’:
      8. 1.1.0.2.8. Help for command ‘/RPKM.Log2’:
    4. 1.1.0.3. Accepted Types
      1. 1.1.0.3.1. /cond
      2. 1.1.0.3.2. Help for command ‘/sid.map’:
      3. 1.1.0.3.3. Help for command ‘/SPCC’:
      4. 1.1.0.3.4. Help for command ‘/Stat.Changes’:
      5. 1.1.0.3.5. Help for command ‘/Statics.Labels’:
      6. 1.1.0.3.6. Help for command ‘/WGCNA’:
    5. 1.1.0.4. Accepted Types
      1. 1.1.0.4.1. /data
      2. 1.1.0.4.2. /anno
      3. 1.1.0.4.3. /mods
      4. 1.1.0.4.4. /out
      5. 1.1.0.4.5. /From.Deseq

GCModeller [version 1.0.0.0]

Module AssemblyName: file:///G:/GCModeller/manual/bin/RNA-seq.exe
Root namespace: RNA_seq.CLI

All of the command that available in this program has been list below:

Function API Info
/Associate.GI
/Clustering
/Co.Vector
/Contacts.Ref
/Data.Frame Generates the data input for the DESeq2 R package.
/DataFrame.RPKMs Merges the RPKM csv data files.
/DEGs
/DEGs.UpDown
/DESeq2
/DOOR.Corrects
/Export.Megan.BIOM
/Export.SAM.Maps
/Export.SSU.Refs
/Export.SSU.Refs.Batch
/Format.GI
/fq2fa
/gast
/gast.stat.names
/Group.n
/HT-seq Count raw reads for DESeq2 analysis.
/Imports.gast.Refs.NCBI_nt
/log2.selects
/PCC
/Rank.Statics
/RPKM
/RPKM.Log2
/sid.map
/SPCC
/Stat.Changes
/Statics.Labels
/WGCNA Generates the cytoscape network model from WGCNA analysis.

Commands


Help for command ‘/Associate.GI’:

Prototype: RNA_seq.CLI::Int32 AssociateGI(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Clustering’:

Prototype: RNA_seq.CLI::Int32 Clustering(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\RNA-seq.exe /Clustering /in <fq> /kmax <int> [/out <out.Csv>]
Example: RNA-seq /Clustering
Help for command ‘/Co.Vector’:

Prototype: RNA_seq.CLI::Int32 CorrelatesVector(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Contacts.Ref’:

Prototype: RNA_seq.CLI::Int32 Contacts(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Data.Frame’:

Prototype: RNA_seq.CLI::Int32 Df(Microsoft.VisualBasic.CommandLine.CommandLine)

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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

Parameters information:

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

Example: /in ""

Accepted Types

/in
Help for command ‘/DataFrame.RPKMs’:

Prototype: RNA_seq.CLI::Int32 MergeRPKMs(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/DEGs’:

Prototype: RNA_seq.CLI::Int32 DEGs(Microsoft.VisualBasic.CommandLine.CommandLine)

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

Prototype: RNA_seq.CLI::Int32 DEGsUpDown(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/DESeq2’:

Prototype: RNA_seq.CLI::Int32 DESeq2(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/DOOR.Corrects’:

Prototype: RNA_seq.CLI::Int32 DOORCorrects(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Export.Megan.BIOM’:

Prototype: RNA_seq.CLI::Int32 ExportToMegan(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Export.SAM.Maps’:

Prototype: RNA_seq.CLI::Int32 ExportSAMMaps(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Export.SSU.Refs’:

Prototype: RNA_seq.CLI::Int32 ExportSSURefs(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Export.SSU.Refs.Batch’:

Prototype: RNA_seq.CLI::Int32 ExportSSUBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Format.GI’:

Prototype: RNA_seq.CLI::Int32 FormatGI(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/fq2fa’:

Prototype: RNA_seq.CLI::Int32 Fq2fa(Microsoft.VisualBasic.CommandLine.CommandLine)

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

Prototype: RNA_seq.CLI::Int32 gastInvoke(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\RNA-seq.exe
Example: RNA-seq /gast
Help for command ‘/gast.stat.names’:

Prototype: RNA_seq.CLI::Int32 StateNames(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Group.n’:

Prototype: RNA_seq.CLI::Int32 GroupN(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/HT-seq’:

Prototype: RNA_seq.CLI::Int32 HTSeqCount(Microsoft.VisualBasic.CommandLine.CommandLine)

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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

Parameters information:

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    [/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 ""

Accepted Types

/Mode
/feature
Help for command ‘/Imports.gast.Refs.NCBI_nt’:

Prototype: RNA_seq.CLI::Int32 ImportsRefFromNt(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/log2.selects’:

Prototype: RNA_seq.CLI::Int32 Log2Selects(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/PCC’:

Prototype: RNA_seq.CLI::Int32 PCC(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\RNA-seq.exe /PCC /expr <expr.matrix.csv> [/out <out.dat>]
Example: RNA-seq /PCC
Help for command ‘/Rank.Statics’:

Prototype: RNA_seq.CLI::Int32 RankStatics(Microsoft.VisualBasic.CommandLine.CommandLine)

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

Prototype: RNA_seq.CLI::Int32 RPKM(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/RPKM.Log2’:

Prototype: RNA_seq.CLI::Int32 Log2(Microsoft.VisualBasic.CommandLine.CommandLine)

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

Parameters information:

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

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

Accepted Types

/cond
Help for command ‘/sid.map’:

Prototype: RNA_seq.CLI::Int32 sIdMapping(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/SPCC’:

Prototype: RNA_seq.CLI::Int32 SPCC(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\RNA-seq.exe /SPCC /expr <expr.matrix.csv> [/out <out.dat>]
Example: RNA-seq /SPCC
Help for command ‘/Stat.Changes’:

Prototype: RNA_seq.CLI::Int32 StatChanges(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Statics.Labels’:

Prototype: RNA_seq.CLI::Int32 MergeLabels(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/WGCNA’:

Prototype: RNA_seq.CLI::Int32 FromWGCNA(Microsoft.VisualBasic.CommandLine.CommandLine)

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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

Parameters information:

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    /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 ""

Accepted Types

/data
/anno
/mods
/out
/From.Deseq