Package: Rmmquant 1.23.0
Zytnicki Matthias
Rmmquant: RNA-Seq multi-mapping Reads Quantification Tool
RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.
Authors:
Rmmquant_1.23.0.tar.gz
Rmmquant_1.23.0.zip(r-4.5)Rmmquant_1.23.0.zip(r-4.4)Rmmquant_1.23.0.zip(r-4.3)
Rmmquant_1.23.0.tgz(r-4.4-arm64)Rmmquant_1.23.0.tgz(r-4.4-x86_64)Rmmquant_1.23.0.tgz(r-4.3-arm64)Rmmquant_1.23.0.tgz(r-4.3-x86_64)
Rmmquant_1.23.0.tar.gz(r-4.5-noble)Rmmquant_1.23.0.tar.gz(r-4.4-noble)
Rmmquant_1.23.0.tgz(r-4.4-emscripten)Rmmquant_1.23.0.tgz(r-4.3-emscripten)
Rmmquant.pdf |Rmmquant.html✨
Rmmquant/json (API)
NEWS
| # Install 'Rmmquant' in R: |
| install.packages('Rmmquant', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Rmmquant-1.23.0(bioc 3.20)Rmmquant-1.22.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:d9d5410bb0
Exports:countsRmmquantClassExampleRmmquantExampleRmmquantRunshow
Dependencies:abindAnnotationDbiapeglmaskpassbase64encbbmlebdsmatrixBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbitbit64bitopsblobbookdownbrewbriobslibcachemcallrclicliprcodacodetoolscolorspacecommonmarkcpp11crayoncredentialscurlDBIDelayedArraydescDESeq2devtoolsdiffobjdigestdownlitellipsisemdbookevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgertggplot2ghgitcredsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrhttr2iniIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellmvtnormnlmenumDerivopensslorg.Mm.eg.dbpillarpkgbuildpkgconfigpkgdownpkgloadplogrplyrpngpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlrematch2remotesrestfulrRhtslibrjsonrlangrmarkdownroxygen2rprojrootRsamtoolsRSQLiterstudioapirtracklayerrversionsS4ArraysS4VectorssassscalessessioninfoshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsyssystemfontsTBX20BamSubsettestthattextshapingtibbletinytexTxDb.Mmusculus.UCSC.mm9.knownGeneUCSC.utilsurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunXMLxml2xopenxtableXVectoryamlzipzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get the counts table of an 'RmmquantClass' object. | counts counts,RmmquantClass-method |
| Rmmquant: RNA-Seq multi-mapping Reads Quantification Tool | Rmmquant |
| An S4 class for Rmmquant. | RmmquantClass-class |
| Example of Rmmquant constructor. | RmmquantClassExample |
| Example of Rmmquant use | RmmquantExample |
| Main Rmmquant function. | RmmquantRun |
| Show the content of an 'RmmquantClass' object. | show,RmmquantClass-method |
| Rmmquant object validation function. | validateRmmquant |
