Uses of Class
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
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Packages that use AbstractModule Package Description fr.ens.biologie.genomique.eoulsan.modules This package define the steps for the Eoulsan workflow.fr.ens.biologie.genomique.eoulsan.modules.chipseq This packages contains the ChIP-Seq modules.fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling This packages contains the peak-calling modules.fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc This packages contains all the quality check modules for ChIP-Seq.fr.ens.biologie.genomique.eoulsan.modules.diffana This package contain all the classes related to the differential analysis step.fr.ens.biologie.genomique.eoulsan.modules.expression This package contain all the classes related to the expression step.fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop This package contain all the classes related to the expression step in hadoop mode.fr.ens.biologie.genomique.eoulsan.modules.expression.local This package contain all the classes related to the expression step in local mode.fr.ens.biologie.genomique.eoulsan.modules.fastqc This package contain all the classes related to FastQC.fr.ens.biologie.genomique.eoulsan.modules.generators This package contain generator steps.fr.ens.biologie.genomique.eoulsan.modules.mapping This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.fr.ens.biologie.genomique.eoulsan.modules.mapping.local This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in local mode.fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop This package contain classes related data management in Hadoop mode.fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload This package contain classes related to upload data to HDFS and Cloud.fr.ens.biologie.genomique.eoulsan.modules.multiqc fr.ens.biologie.genomique.eoulsan.modules.singlecell -
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Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules Modifier and Type Class Description class
CheckerModule
This class is a module that launch checkers.class
CopyInputDataModule
Copy input files of a format in another location or in different compression format.class
CopyOutputDataModule
Copy output files of a step with a specified format to the output directory.class
DesignModule
This class define a design module.class
FailModule
This module is a module that always fails.class
FakeModule
This module is a fake module.class
FirstModule
This class define a first module that do nothing.class
GalaxyToolModule
The Class GalaxyToolStep.class
ImportModule
This class define a import step.class
MergerModule
This class define a generic merger module.class
RequirementInstallerModule
This class allow to install a requirement.class
ShellModule
This class define a module that execute a shell command.class
SplitterModule
This class define a generic splitter module.class
TechnicalReplicateMergerModule
This class define a merger module for technical replicates.class
TerminalModule
This class define a terminal task that do nothing. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.chipseq
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.chipseq Modifier and Type Class Description class
MergeInputRepLocalModule
This class merges SAM files of input of the same experiment.class
RmDupLocalModule
This class removes PCR duplicates from a SAM file.class
TrackHubModule
This class construct TrackHub for genome browser visualization. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling Modifier and Type Class Description class
BedToolsModule
This class uses tools from the BEDTools suite.class
DeepToolsModule
This class uses tools from the DeepTools suite.class
MACS2Module
This class defines the macs2 peak-calling step.class
MergePeaksModule
This class defines the peak merging step. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc Modifier and Type Class Description class
CountSplicedReadsModule
This step computes how many spliced alignments there are in a SAM file.class
IDRModule
This class defines the IDR quality check step. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.diffana
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.diffana Modifier and Type Class Description class
DESeq2Module
Class to run the differential analysis with DEseq2class
DiffAnaModule
This class define the module of differential analysis in local mode.class
DiffanaResultsAnnotationModule
This class define a module that create annotated expression files in TSV, ODS or XLSX format.class
NormalizationModule
This class define the module for normalization -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.expression
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.expression Modifier and Type Class Description class
AbstractExpressionModule
This abstract class define and parse arguments for the expression module.class
ExpressionResultsAnnotationModule
This class define a module that create annotated expression files in TSV, ODS or XLSX format. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop Modifier and Type Class Description class
ExpressionHadoopModule
This class is the main class for the expression program of the reads in hadoop mode. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.expression.local
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.expression.local Modifier and Type Class Description class
ExpressionLocalModule
This class is the module to compute expression in local mode -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.fastqc
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.fastqc Modifier and Type Class Description class
FastQCModule
This class define a module that compute QC report using FastQC. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.generators
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.generators Modifier and Type Class Description class
DummyGeneratorModule
This class implements a dummy generator module that create an empty file.class
GenericStorageGeneratorModule
This module allow to easily store output of generator to avoid computation at each Eoulsan startup.class
GenomeDescriptionGeneratorModule
This class implements a genome description generator module.class
GenomeMapperIndexGeneratorModule
This class define a module that generate a genome mapper index.class
GFFFastaGeneratorModule
This generator allow to generate a genome fasta file from the fasta section of a GFF file.class
Minimap2IndexGeneratorModule
This class define a module that generate a Minimap2 mapper index.class
STARIndexGeneratorModule
This class define a module that generate a STAR mapper index. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mapping
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mapping Modifier and Type Class Description class
AbstractBAM2SAMModule
This class define a module for converting BAM files into SAM.class
AbstractFilterAndMapReadsModule
This class define an abstract module for read filtering, mapping and alignments filtering.class
AbstractReadsFilterModule
This class define an abstract module for read filtering.class
AbstractReadsMapperModule
This class define an abstract module for read mapping.class
AbstractSAM2BAMModule
This class define a module for converting SAM files into BAM.class
AbstractSAM2FASTQModule
This class define a module for converting SAM files into BAM.class
AbstractSAMFilterModule
This class define an abstract module for alignments filtering.class
AbstractSplice2BEDModule
This class define a module for converting SAM files into BED. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop Modifier and Type Class Description class
FilterAndMapReadsHadoopModule
This class define a Step that filter and map read in Hadoop mode.class
ReadsFilterHadoopModule
This class is the main class for the filter reads program in hadoop mode.class
ReadsMapperHadoopModule
This class define an mapper module in Hadoop mode.class
SAM2BAMHadoopModule
This class define a module for converting SAM files into BAM.class
SAMFilterHadoopModule
This class define a filter alignment step in Hadoop mode. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mapping.local Modifier and Type Class Description class
BAM2SAMLocalModule
This class define a module for converting BAM files into SAM.class
ReadsFilterLocalModule
This class define a module for reads filtering.class
ReadsMapperLocalModule
This class define a module for reads mapping.class
SAM2BAMLocalModule
This class define a module for converting SAM files into BAM.class
SAM2FASTQLocalModule
This class define a module for converting SAM files into FASTQ.class
SAMFilterLocalModule
This class define a Step for alignments filtering.class
Splice2BEDModule
This class define a module for converting SAM files into BED. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop Modifier and Type Class Description class
CopyDesignAndWorkflowFilesToOutputModule
This module copy design and workflow file to output directory. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload Modifier and Type Class Description class
DefineDataFormatToDownload
This Step allow to define the list of the formats of the files to download at the end of a Hadoop execution.class
HadoopUploadModule
This class define a module for Hadoop file uploading.class
HDFSDataDownloadModule
This class define a download module that retrieve data from HDFS at the end of an analysis.class
LocalUploadModule
This class define a Step for local mode file uploading.class
UploadModule
This class define a abstract module class for files uploading. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.multiqc
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.multiqc Modifier and Type Class Description class
MultiQCModule
This class define a module for MultiQC. -
Uses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.singlecell
Subclasses of AbstractModule in fr.ens.biologie.genomique.eoulsan.modules.singlecell Modifier and Type Class Description class
ExpressionToMatrixModule
This class define a class that allow to merge expression file into a matrix file.class
MatrixToCellRangerMatrixModule
This class define a class that allow to create a Cell Ranger matrix from an existing matrix file.class
RSingleCellExperimentCreatorModule
This class define a class that allow to create a SingleCellExperiment Bioconductor Object and save it as a RDS file.
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