Package: maser 1.31.0

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_1.31.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
maser/json (API)

# Install 'maser' in R:
install.packages('maser', repos = c('https://bioc.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 3 mentions 21 exports 150 dependencies

Last updated from:961d6ab1be. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR241
linux-devel-x86_64NOTE462
source / vignettesOK383
linux-release-x86_64NOTE544
macos-release-arm64NOTE274
macos-oldrel-arm64NOTE254
windows-develNOTE429
windows-releaseNOTE399
windows-oldrelNOTE404
wasm-releaseOK225

Exports:annotationavailableFeaturesUniprotKBboxplot_PSI_levelscountsdisplaydotplotfilterByCoveragefilterByEventIdgeneEventsmapProteinFeaturesToEventsmapTranscriptsToEventsmaserpcaplotGenePSIplotTranscriptsplotUniprotKBFeaturesPSIsplicingDistributionsummarytopEventsvolcano

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrDTensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslotelpillarpkgconfigplyrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Introduction
Overview of maser | Importing rMATS events | Filtering events | Global splicing plots | Genomic visualization of splicing events | Exon skipping | Intron retention | Mutually exclusive exons | Alternative 5' and 3' exons | Session info
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

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

Mapping protein features to splicing events
Overview of protein annotation | Annotation of protein features | Creating the maser object | Query available protein features at Uniprot | Steps for annotation | SRSF6 example | RIPK2 example | Session info
Rendered fromProtein_mapping.Rmdusingknitr::rmarkdown

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