Package: maser 1.30.0

Diogo F.T. Veiga

maser: Mapping Alternative Splicing Events to pRoteins

This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.

Authors:Diogo F.T. Veiga [aut, cre]

maser_1.30.0.tar.gz
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maser_1.30.0.tgz(r-4.6-any)maser_1.30.0.tgz(r-4.5-any)
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maser_1.30.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
maser/json (API)
NEWS

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

Bug tracker:https://github.com/diogoveiga/maser/issues

On BioConductor:maser-1.31.0(bioc 3.24)maser-1.30.0(bioc 3.23)

alternativesplicingtranscriptomicsvisualization

7.18 score 21 stars 27 scripts 522 downloads 3 mentions 21 exports 149 dependencies

Last updated from:c8518e13e3 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

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source / vignettesOK356
linux-release-x86_64NOTE462
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Exports:annotationavailableFeaturesUniprotKBboxplot_PSI_levelscountsdisplaydotplotfilterByCoveragefilterByEventIdgeneEventsmapProteinFeaturesToEventsmapTranscriptsToEventsmaserpcaplotGenePSIplotTranscriptsplotUniprotKBFeaturesPSIsplicingDistributionsummarytopEventsvolcano

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrDTensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslotelpillarpkgconfigplyrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Introduction

Diogo Veiga

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2018-07-20
Started: 2018-02-28

Mapping protein features to splicing events

Diogo Veiga

Rendered fromProtein_mapping.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2018-07-20
Started: 2018-03-29

Readme and manuals

Help Manual

Help pageTopics
Retrieve annotation of splicing events from a maser object.annotation,Maser-method
Query available human protein features in UniprotKB.availableFeaturesUniprotKB
Boxplots of PSI distributions by splicing type.boxplot_PSI_levels
Retrieve raw read counts values from a maser object.counts,Maser-method
Visualization of splicing events annotation using an interactive data table.display
Dotplot representation of splicing events.dotplot
Filter splicing events based on coverage.filterByCoverage
Filter splicing events based on event identifier and type.filterByEventId
Retrieve splicing events for a given gene.geneEvents
Retrieve genomic ranges of splicing events from a maser object.granges,Maser-method
Mapping of splice events to UniprotKB protein features.mapProteinFeaturesToEvents
Mapping of splice events to Ensembl transcripts.mapTranscriptsToEvents
Create a maser object by importing rMATS splicing events.maser
S4 class to represent splicing events imported from rMATS.Maser-class
Prinicipal component analysis of PSI distributions.pca
Boxplots of Percent spliced-in levels for gene events.plotGenePSI
Mapping and visualization of Ensembl transcripts affected by splicing.plotTranscripts
Mapping and visualization of UniprotKB protein features affected by splicing.plotUniprotKBFeatures
Retrieve PSI (percent spliced in) values from a maser object.PSI
Retrieve PSI (percent spliced in) values from a maser object.PSI,Maser,character-method
Proportion of events by splicing type.splicingDistribution
Retrieve rMATS stats of differential splicing from a maser object.summary,Maser-method
Filter splicing events based on false discovery rate and PSI change.topEvents
Volcano plot of splicing events.volcano