Package: metaseqR2 1.19.0

Panagiotis Moulos

metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Authors:Panagiotis Moulos [aut, cre]

metaseqR2_1.19.0.tar.gz
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metaseqR2.pdf |metaseqR2.html✨
metaseqR2/json (API)
NEWS

# Install 'metaseqR2' in R:
install.packages('metaseqR2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pmoulos/metaseqr2/issues

Datasets:
  • hg19pvalues - P-values from human RNA-Seq data with two conditions, four samples
  • libsizeListMm9 - Mouse RNA-Seq data with two conditions, four samples
  • mm9GeneCounts - Mouse RNA-Seq data with two conditions, four samples
  • sampleListMm9 - Mouse RNA-Seq data with two conditions, four samples

On BioConductor:metaseqR2-1.17.0(bioc 3.20)metaseqR2-1.16.0(bioc 3.19)

softwaregeneexpressiondifferentialexpressionworkflowsteppreprocessingqualitycontrolnormalizationreportwritingrnaseqtranscriptionsequencingtranscriptomicsbayesianclusteringcellbiologybiomedicalinformaticsfunctionalgenomicssystemsbiologyimmunooncologyalternativesplicingdifferentialsplicingmultiplecomparisontimecoursedataimportatacseqepigeneticsregressionproprietaryplatformsgenesetenrichmentbatcheffectchipseq

6.05 score 7 stars 4 scripts 202 downloads 1 mentions 54 exports 228 dependencies

Last updated 18 days agofrom:22e1b2933d. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:buildAnnotationDatabasebuildCustomAnnotationcombineBonferronicombineHarmoniccombineMaxpcombineMinpcombineSimescombineWeightcreateSignalTracksdiagplotAvgFtddiagplotBoxplotdiagplotCordiagplotDeHeatmapdiagplotEdaseqdiagplotFiltereddiagplotFtddiagplotMdsdiagplotNoiseqdiagplotPairsdiagplotRocdiagplotVenndiagplotVolcanodownsampleCountsestimateAufcWeightsestimateSimParamsgetAnnotationgetDefaultsgetInstalledAnnotationsgetWeightsimportCustomAnnotationloadAnnotationmakeSimDataSdmakeSimDataTccmetaseqr2metaseqrPlotmetaTestnormalizeAbsseqnormalizeDeseqnormalizeDeseq2normalizeDssnormalizeEdaseqnormalizeEdgernormalizeNbpseqnormalizeNoiseqread2countreadTargetsstatAbsseqstatDeseqstatDeseq2statDssstatEdgerstatLimmastatNbpseqstatNoiseq

Dependencies:abindABSSeqaffyaffyioannotateAnnotationDbiaroma.lightaskpassassertthatassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbookdownbootstrapBSgenomebslibbsseqcacachemcallrcaToolsclasscliclustercodetoolscolorspacecorrplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdendextendDESeq2diagramdigestdplyrDSSDTEDASeqedgeReggevaluatefansifarverfastmapfilelockFMStablefontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygclusgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2globalsgluegplotsgridExtragtablegtoolsharmonicmeanpHDF5Arrayheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2hwriterinterpipredIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelatticeExtralavalazyevallifecyclelimmalistenvlocfitlog4rmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellNBPSeqnlmennetnumDerivopensslpanderparallellypermutepillarpkgconfigplogrplotlyplyrpngpreprocessCoreprettyunitsprocessxprodlimprogressprogressrpromisespspurrrpwalignqapqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlregistryreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrmdformatsrmetarpartRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesseriationshapeShortReadsnowSparseArraysparseMatrixStatsSQUAREMstatmodstringistringrSummarizedExperimentSuppDistssurvcompsurvivalsurvivalROCsystibbletidyrtidyselecttinytexTSPtxdbmakerUCSC.utilsutf8vctrsveganVennDiagramviridisviridisLitevsnwebshotwithrxfunXMLxml2xtableXVectoryamlzlibbioczoo

Building an annotation database for metaseqR2

Panagiotis Moulos

Rendered frommetaseqr2-annotation.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-03-07
Started: 2019-09-23

Usage of the metaseqR2 package

Panagiotis Moulos

Rendered frommetaseqr2-statistics.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-10-06
Started: 2019-09-23

Readme and manuals

Help Manual

Help pageTopics
Build a local annotation database for metaseqR2buildAnnotationDatabase
Import custom annotation to the metaseqR2 annotation database from GTF filebuildCustomAnnotation
Combine p-values with Bonferroni's methodcombineBonferroni
Combine p-values using weightscombineHarmonic
Combine p-values using the maximum p-valuecombineMaxp
Combine p-values using the minimum p-valuecombineMinp
Combine p-values with Simes' methodcombineSimes
Combine p-values using weightscombineWeight
Create bigWig signal trackscreateSignalTracks
Create average False (or True) Discovery curvesdiagplotAvgFtd
Boxplots wrapper for the metaseqR2 packagediagplotBoxplot
Summarized correlation plotsdiagplotCor
Diagnostic heatmap of differentially expressed genesdiagplotDeHeatmap
Diagnostic plots based on the EDASeq packagediagplotEdaseq
Diagnostic plot for filtered genesdiagplotFiltered
Create False (or True) Positive (or Negative) curvesdiagplotFtd
Multi-Dimensinal Scale plots or RNA-Seq samplesdiagplotMds
Diagnostic plots based on the NOISeq packagediagplotNoiseq
Massive X-Y, M-D correlation plotsdiagplotPairs
Create basic ROC curvesdiagplotRoc
Venn diagrams when performing meta-analysisdiagplotVenn
(Interactive) volcano plots of differentially expressed genesdiagplotVolcano
Downsample read countsdownsampleCounts
Estimate AUFC weightsestimateAufcWeights
Estimate negative binomial parameters from real dataestimateSimParams
Annotation downloadergetAnnotation
Default parameters for several metaseqr functionsgetDefaults
Load a metaseqR2 annotation elementgetInstalledAnnotations
Get precalculated statistical test weightsgetWeights
p-values from human RNA-Seq data with two conditions, four sampleshg19pvalues
Import a metaseqR2 custom annotation elementimportCustomAnnotation
Mouse RNA-Seq data with two conditions, four sampleslibsizeListMm9
Load a metaseqR2 annotation elementloadAnnotation
Create simulated counts using the Soneson-Delorenzi methodmakeSimDataSd
Create simulated counts using TCC packagemakeSimDataTcc
The main metaseqr2 pipelinemetaseqr2
Diagnostic plots for the metaseqR2 packagemetaseqrPlot
Meta-analysis using several RNA-Seq statisticsmetaTest
Mouse RNA-Seq data with two conditions, four samplesmm9GeneCounts
Normalization based on the ABSSeq packagenormalizeAbsseq
Normalization based on the DESeq packagenormalizeDeseq
Normalization based on the DESeq2 packagenormalizeDeseq2
Normalization based on the DSS packagenormalizeDss
Normalization based on the EDASeq packagenormalizeEdaseq
Normalization based on the edgeR packagenormalizeEdger
Normalization based on the NBPSeq packagenormalizeNbpseq
Normalization based on the NOISeq packagenormalizeNoiseq
SAM/BAM/BED file reader helper for the metaseqr2 pipelineread2count
Creates sample list and BAM/BED file list from filereadTargets
Mouse RNA-Seq data with two conditions, four samplessampleListMm9
Statistical testing with ABSSeqstatAbsseq
Statistical testing with DESeqstatDeseq
Statistical testing with DESeq2statDeseq2
Statistical testing with DSSstatDss
Statistical testing with edgeRstatEdger
Statistical testing with limmastatLimma
Statistical testing with NBPSeqstatNbpseq
Statistical testing with NOISeqstatNoiseq