Package: IntEREst 1.29.0
IntEREst: Intron-Exon Retention Estimator
This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).
Authors:
IntEREst_1.29.0.tar.gz
IntEREst_1.29.0.zip(r-4.5)IntEREst_1.29.0.zip(r-4.4)IntEREst_1.29.0.zip(r-4.3)
IntEREst_1.29.0.tgz(r-4.4-any)IntEREst_1.29.0.tgz(r-4.3-any)
IntEREst_1.29.0.tar.gz(r-4.5-noble)IntEREst_1.29.0.tar.gz(r-4.4-noble)
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IntEREst.pdf |IntEREst.html✨
IntEREst/json (API)
NEWS
# Install 'IntEREst' in R: |
install.packages('IntEREst', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- mdsChr22ExObj - Object of SummarizedExperiment type for exon-exon junction of MDS data
- mdsChr22IntSpObj - Object of SummarizedExperiment type for intron spanning reads of MDS data
- mdsChr22Obj - Object of SummarizedExperiment type for intron retention MDS data
- pwmU12db - PWM of U12 and U2-type introns splice sites
- u12 - U12 data
On BioConductor:IntEREst-1.29.0(bioc 3.20)IntEREst-1.28.0(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:c53a1fd4d5
Exports:addAnnotationannotateU12applyOverlapbuildSsTypePwmscountscounts.InterestResultsdeseqInterestDEXSeqIntEREstexactTestInterestgetAnnotationgetRepeatTableglmInterestinterestinterest.sequentialInterestResultinterestResultIntExintexBoxplotintexIndexlfcmergeInterestResultpsiqlfInterestreadInterestResultsreferencePreparescaledRetentionsubInterestResulttreatInterestu12Boxplotu12BoxplotNbu12DensityPlotu12DensityPlotIntronu12Indexu12NbIndexunionRefTrupdateRowDataCol
Dependencies:abindade4annotateAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArrayDESeq2DEXSeqdigestdplyredgeRfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegtablehmshttrhttr2hwriterIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpixmappkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRMySQLRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessegmentedseqinrseqLogosnowspSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLxml2xtableXVectoryamlzlibbioc