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Release: Showing tree for 3.23

AnnotationData(938)

ChipManufacturer(404)

AffymetrixChip(342)

AgilentChip(17)

ClonetechChip(0)

CodelinkChip(12)

GEChip(0)

INDACChip(1)

IlluminaChip(29)

QiagenChip(1)

RNG_MRCChip(2)

RocheChip(0)

UniversityHealthNetwork(0)

ChipName(197)

HuO22(1)

JazaerimetaData(0)

Mu15v1(1)

Mu22v3(1)

Norway981(1)

OperonHumanV3(1)

PartheenMetaData(1)

Roberts2005Annotation(1)

SHDZ(1)

adme16cod(1)

ag(3)

ath1121501(4)

celegans(3)

drosgenome1(3)

drosophila2(3)

h10kcod(1)

h20kcod(1)

hcg110(3)

hcgi12k(0)

hcgi8k(0)

hgfocus(3)

hgu133a(4)

hgu133a2(4)

hgu133b(3)

hgu133plus2(4)

hgu95a(3)

hgu95av2(4)

hgu95b(3)

hgu95c(3)

hgu95d(3)

hgu95e(3)

hguatlas13k(1)

hgug4100a(1)

hgug4101a(1)

hgug4110b(1)

hgug4111a(1)

hgug4112a(1)

hguqiagenv3(1)

hi16cod(1)

hs25kresogen(1)

hu35ksuba(3)

hu35ksubb(3)

hu35ksubc(3)

hu35ksubd(3)

hu6800(3)

hwgcod(1)

indac(1)

lumiHumanV1(0)

lumiHumanV2(0)

lumiMouseV1(0)

lumiRatV1(0)

m10kcod(1)

m20kcod(1)

mgu74a(3)

mgu74av2(3)

mgu74b(3)

mgu74bv2(3)

mgu74c(3)

mgu74cv2(3)

mguatlas5k(1)

mgug4121a(1)

mgug4122a(1)

mi16cod(1)

mm24kresogen(1)

moe430a(3)

moe430b(3)

mouse4302(4)

mouse430a2(4)

mpedbarray(1)

mu11ksuba(3)

mu11ksubb(3)

mu19ksuba(2)

mu19ksubb(2)

mu19ksubc(2)

mwgcod(1)

pedbarrayv10(1)

pedbarrayv9(1)

r10kcod(1)

rae230a(3)

rae230b(3)

rat2302(4)

rgu34a(3)

rgu34b(3)

rgu34c(3)

rgug4130a(1)

ri16cod(1)

rnu34(3)

rtu34(3)

rwgcod(1)

u133x3p(3)

xenopuslaevis(2)

yeast2(3)

ygs98(4)

zebrafish(3)

CustomArray(2)

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GACustomCDF(0)

MBNICustomCDF(0)

CustomDBSchema(10)

GeneCardsCustomSchema(0)

FunctionalAnnotation(30)

Organism(672)

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Apis_mellifera(4)

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Arabidopsis_thaliana(15)

Asparagus_officinalis(1)

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Caenorhabditis_elegans(12)

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Canis_familiaris(16)

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Drosophila_melanogaster(17)

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Glycine_max(1)

Homo_sapiens(259)

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Mus_musculus(117)

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Sus_scrofa(10)

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Zea_mays(2)

PackageType(655)

AnnotationHub(43)

BSgenome(111)

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FRMA(12)

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MeSHDb(2)

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TxDb(50)

XtraSNPlocs(2)

cdf(118)

db0(19)

probe(98)

SequenceAnnotation(5)

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ExpressionData(89)

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OvarianCancerData(3)

ProstateCancerData(7)

HIVData(1)

OrganismData(165)

Anopheles_gambiae_Data(0)

Apis_mellifera_Data(0)

Arabidopsis_lyrata_Data(0)

Arabidopsis_thaliana_Data(6)

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Caenorhabditis_elegans_Data(2)

Callithrix_jacchus_Data(0)

Canis_familiaris_Data(0)

Ciona_intestinalis_Data(0)

Danio_rerio_Data(4)

Drosophila_melanogaster_Data(8)

Drosophila_virilis_Data(0)

Eremothecium_gossypii_Data(0)

Escherichia_coli_Data(4)

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Gasterosteus_aculeatus_Data(0)

Glycine_max_Data(0)

Homo_sapiens_Data(123)

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Kluyveromyces_lactis_Data(0)

Macaca_mulatta_Data(0)

Magnaporthe_grisea_Data(0)

Medicago_truncatul_Data(0)

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Mus_musculus_Data(31)

Neurospora_crassa_Data(0)

Oncorhynchus_mykiss_Data(0)

Oryza_sativa_Data(0)

Pan_paniscus_Data(0)

Pan_troglodytes_Data(2)

Plasmodium_falciparum_Data(0)

Pseudomonas_aeruginosa_Data(2)

Rattus_norvegicus_Data(6)

Saccharomyces_cerevisiae_Data(12)

Saccharum_officinarum_Data(0)

Schizosaccharomyces_pombe_Data(0)

Staphylococcus_aureus_Data(2)

Sus_scrofa_Data(0)

Taeniopygia_guttata_Data(0)

Triticum_aestivum_Data(0)

Vitis_vinifera_Data(0)

Xenopus_laevis_Data(0)

Xenopus_tropicalis_Data(0)

Zea_mays_Data(0)

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ExperimentHub(115)

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ArrayExpress(14)

ENCODE(7)

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NCI(9)

PathwayInteractionDatabase(2)

Project1000genomes(3)

ReproducibleResearch(38)

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CellCulture(13)

Genome(69)

Germline(0)

Proteome(12)

Somatic(2)

StemCell(8)

Tissue(47)

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CGHData(4)

FlowCytometryData(5)

HighThroughputImagingData(4)

MassSpectrometryData(26)

ImagingMassSpectrometryData(1)

MicroarrayData(132)

ChipOnChipData(11)

GenotypingArrayData(0)

MethylationArrayData(24)

MicroRNAArrayData(0)

MultiChannelData(1)

OneChannelData(3)

ProprietaryPlatformsData(0)

ReversePhaseProteinArrayData(0)

TissueMicroarrayData(17)

TwoChannelData(5)

mRNAArrayData(0)

MicrotitrePlateAssayData(1)

SAGEData(1)

SequencingData(169)

ChIPSeqData(17)

DNASeqData(9)

ExomeSeqData(0)

MethylSeqData(2)

MicrobiomeData(12)

RIPSeqData(0)

RNASeqData(79)

SangerSeqData(0)

SingleCellData(41)

SmallRNAData(1)

SpatialData(13)

miRNAData(7)

qPCRData(4)

Software(2,618)

AssayDomain(970)

CellBasedAssays(67)

ChIPchip(6)

CopyNumberVariation(66)

CpGIsland(12)

DNAMethylation(121)

ExonArray(12)

GeneExpression(643)

GeneticVariability(41)

SNP(90)

Transcription(186)

aCGH(9)

BiologicalQuestion(1,034)

AlternativeSplicing(51)

Coverage(165)

DNA3DStructure(13)

DemethylateRegionDetection(0)

DenovoAssembler(0)

DifferentialDNA3DStructure(0)

DifferentialExpression(400)

DifferentialMethylation(63)

DifferentialPeakCalling(16)

DifferentialSplicing(38)

DriverMutation(2)

FunctionalPrediction(36)

GeneFusionDetection(2)

GenePrediction(28)

GeneRegulation(119)

GeneSetEnrichment(173)

GeneSignaling(13)

GeneTarget(48)

GenomeAnnotation(55)

GenomeAssembly(13)

GenomeWideAssociation(34)

GenomicVariation(42)

GermlineMutation(1)

HistoneModification(11)

IndelDetection(2)

LinkageDisequilibrium(5)

MetagenomeAssembly(0)

MicrosatelliteDetection(0)

MotifAnnotation(26)

MotifDiscovery(15)

NetworkEnrichment(52)

NetworkInference(62)

NucleosomePositioning(10)

PeakDetection(24)

QuantitativeTrailLocus(0)

Scaffolding(0)

SequenceMatching(55)

SomaticMutation(25)

SplicedAlignment(6)

StructuralVariation(3)

TranscriptomeVariant(6)

VariantAnnotation(35)

VariantDetection(13)

Infrastructure(615)

DataImport(349)

DataRepresentation(162)

GPU(1)

GUI(68)

ResearchField(1,389)

Agroinformatics(0)

BiomedicalInformatics(87)

Biophysics(0)

CellBiology(69)

Cheminformatics(19)

ComparativeGenomics(13)

ComputationalChemistry(0)

Epigenetics(108)

Epitranscriptomics(4)

FunctionalGenomics(107)

Genetics(407)

Immunology(426)

ImmunoOncology(426)

ImmunoPrevention(0)

Immunogenetics(1)

Lipidomics(14)

MathematicalBiology(10)

Metabolomics(124)

Metagenomics(38)

Pharmacogenetics(16)

Pharmacogenomics(19)

Phylogenetics(16)

Proteomics(193)

StructuralGenomics(1)

StructuralPrediction(12)

SystemsBiology(100)

Transcriptomics(298)

ShinyApps(40)

StatisticalMethod(884)

Bayesian(91)

Classification(188)

Clustering(296)

DecisionTree(8)

DimensionReduction(94)

FeatureExtraction(68)

GraphAndNetwork(131)

HiddenMarkovModel(16)

MultidimensionalScaling(5)

NeuralNetwork(5)

PatternLogic(3)

PrincipalComponent(59)

Regression(156)

StructuralEquationModels(1)

SupportVectorMachine(11)

Survival(47)

TimeCourse(55)

Technology(1,611)

AnnotationHubSoftware(5)

CRISPR(24)

ExperimentHubSoftware(11)

FlowCytometry(72)

MassSpectrometry(154)

ImagingMassSpectrometry(3)

Microarray(399)

ChipOnChip(12)

OneChannel(67)

ProprietaryPlatforms(11)

ReversePhaseProteinArray(0)

TissueMicroarray(2)

TwoChannel(59)

mRNAMicroarray(24)

MicrotitrePlateAssay(14)

SAGE(7)

Sequencing(938)

ATACSeq(38)

ChIPSeq(94)

DNASeq(41)

DNaseSeq(9)

DenovoGenome(0)

DenovoTranscriptome(0)

ExomeSeq(7)

HiC(36)

LongRead(7)

MNaseSeq(2)

MethylSeq(35)

MicrobialStrain(1)

Microbiome(57)

PooledScreens(6)

RIPSeq(5)

RNASeq(422)

RiboSeq(11)

SangerSeq(3)

SmallRNA(4)

TargetedResequencing(6)

WholeGenome(40)

miRNA(17)

SingleCell(346)

Spatial(87)

ddPCR(5)

qPCR(13)

WorkflowManagement(1)

WorkflowStep(1,321)

Alignment(109)

MultipleSequenceAlignment(19)

Annotation(152)

BatchEffect(76)

ExperimentalDesign(34)

GenomeBrowsers(2)

MultipleComparison(184)

Normalization(188)

Pathways(207)

BioCarta(5)

GO(76)

KEGG(55)

NCINatureCurated(0)

Reactome(22)

Preprocessing(276)

QualityControl(245)

ReportWriting(39)

Visualization(614)

Network(167)

Workflow(37)

AnnotationWorkflow(4)

BasicWorkflow(5)

DifferentialSplicingWorkflow(0)

EpigeneticsWorkflow(6)

GeneExpressionWorkflow(13)

GenomicVariantsWorkflow(0)

ImmunoOncologyWorkflow(20)

ProteomicsWorkflow(1)

ResourceQueryingWorkflow(2)

SingleCellWorkflow(10)

SpatialWorkflow(1)

WorkflowManagement

1 package

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Package	Category	Version	Status
systemPipeRBioc systemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis	software	2.18.0	current