Uses of Class
fr.ens.biologie.genomique.eoulsan.annotations.LocalOnly
-
Packages that use LocalOnly Package Description fr.ens.biologie.genomique.eoulsan.data.protocols This package contains class for protocols used by theDataFile
classes.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.local This package contain all the classes related to the expression step in local mode.fr.ens.biologie.genomique.eoulsan.modules.generators This package contain generator steps.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.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 -
-
Uses of LocalOnly in fr.ens.biologie.genomique.eoulsan.data.protocols
Classes in fr.ens.biologie.genomique.eoulsan.data.protocols with annotations of type LocalOnly Modifier and Type Class Description class
FTPURLDataProtocol
This class define the ftp protocol in local mode.class
HTTPSURLDataProtocol
This class define the http protocol in local mode.class
HTTPURLDataProtocol
This class define the http protocol in local mode. -
Uses of LocalOnly in fr.ens.biologie.genomique.eoulsan.modules
Classes in fr.ens.biologie.genomique.eoulsan.modules with annotations of type LocalOnly 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
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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.chipseq
Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq with annotations of type LocalOnly 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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling with annotations of type LocalOnly 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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc
Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc with annotations of type LocalOnly 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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.diffana
Classes in fr.ens.biologie.genomique.eoulsan.modules.diffana with annotations of type LocalOnly 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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.expression.local
Classes in fr.ens.biologie.genomique.eoulsan.modules.expression.local with annotations of type LocalOnly Modifier and Type Class Description class
ExpressionLocalModule
This class is the module to compute expression in local mode -
Uses of LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.generators
Classes in fr.ens.biologie.genomique.eoulsan.modules.generators with annotations of type LocalOnly Modifier and Type Class Description class
GenericStorageGeneratorModule
This module allow to easily store output of generator to avoid computation at each Eoulsan startup.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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping.local with annotations of type LocalOnly Modifier and Type Class Description 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. -
Uses of LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
Classes in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with annotations of type LocalOnly Modifier and Type Class Description class
LocalUploadModule
This class define a Step for local mode file uploading. -
Uses of LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.multiqc
Classes in fr.ens.biologie.genomique.eoulsan.modules.multiqc with annotations of type LocalOnly Modifier and Type Class Description class
MultiQCModule
This class define a module for MultiQC. -
Uses of LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.singlecell
Classes in fr.ens.biologie.genomique.eoulsan.modules.singlecell with annotations of type LocalOnly 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.
-