Package: SpliceWiz 1.9.0

Alex Chit Hei Wong

SpliceWiz: interactive analysis and visualization of alternative splicing in R

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.

Authors:Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb], William Ritchie [cph]

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SpliceWiz.pdf |SpliceWiz.html✨
SpliceWiz/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/alexchwong/splicewiz/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On BioConductor:SpliceWiz-1.9.0(bioc 3.21)SpliceWiz-1.8.0(bioc 3.20)

softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp

6.41 score 16 stars 8 scripts 311 downloads 112 exports 182 dependencies

Last updated 2 months agofrom:878444951f. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-win-x86_64NOTEDec 18 2024
R-4.5-linux-x86_64NOTEDec 18 2024
R-4.4-win-x86_64NOTEDec 18 2024
R-4.4-mac-x86_64NOTEDec 18 2024
R-4.4-mac-aarch64NOTEDec 18 2024
R-4.3-win-x86_64NOTEDec 18 2024
R-4.3-mac-x86_64NOTEDec 18 2024
R-4.3-mac-aarch64NOTEDec 18 2024

Exports:addPSI_edgeRapplyFiltersASE_DESeqASE_DoubleExpSeqASE_edgeRASE_edgeR_timeseriesASE_limmaASE_limma_timeseriesASEFilterassayassay<-assayNamesassayNames<-assaysassays<-BAM2COVbuildFullRefbuildRefcalculateMappabilitycbindcoercecolDatacolData<-collateDataconditioncoord2GRcovfilecovfile<-down_excdown_exc<-down_incdown_inc<-extract_gene_ids_for_GOfindBAMSfindFASTQfindSamplesfindSpliceWizOutputfitASE_edgeRfitASE_edgeR_customgenerateSyntheticReadsgetAvailableGOgetCoveragegetCoverage_DFgetCoverageBinsgetCoverageDatagetCoverageRegionsgetDefaultFiltersgetExonRangesgetGenomeDatagetNonPolyARefgetPlotObjectgetResourcesgoASEgoGenesisCOVjunc_countsjunc_counts_unsjunc_grjunc_PSImakeMatrixmakeMeanPSImakeSEplotAnnoTrackplotCoverageplotGenomeplotGOplotViewprocessBAMrbindrealize_NxtSErefrow_grrowDatarowData<-runFiltersampleQCsampleQC<-setResolutionsetSWthreadsshowEventsshowExonssourcePathspliceWizSpliceWiz_example_bamsSpliceWiz_example_NxtSESTAR_alignExperimentSTAR_alignReadsSTAR_buildGenomeSTAR_buildRefSTAR_loadGenomeGTFSTAR_mappabilitySTAR_versionsubset_EventNames_by_GOtestASE_edgeRtheme_whitetheme_white_legendtheme_white_legend_plot_tracktracksup_excup_exc<-up_incup_inc<-update_NxtSEviewASEviewExonsviewGenesviewGOviewIntronsviewIRviewIR_NMDviewProteinsviewTranscripts

Dependencies:abindannotateAnnotationDbiAnnotationHubaskpassassertthatbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebslibcacachemcallrcliclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdendextenddigestdplyrDTeggevaluateExperimentHubfansifarverfastmapfilelockfontawesomeforeachformatRfsfstfstcorefutile.loggerfutile.optionsgclusgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridExtragtableHDF5ArrayheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeNxtIRFdataompBAMopensslpatchworkpermutepheatmappillarpkgconfigplogrplotlyplyrpngprettyunitsprocessxprogresspromisespspurrrqapR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppProgressRCurlregistryreshape2restfulrrhandsontablerhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorssassscalesselectrseriationshinyshinydashboardshinyFilesshinyWidgetssnowsourcetoolsSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTSPUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2xtableXVectoryamlzlibbioc

SpliceWiz: Quick Start

Alex CH Wong

Rendered fromSW_QuickStart.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-03-12
Started: 2022-05-11

SpliceWiz: the cookbook

Alex CH Wong

Rendered fromSW_Cookbook.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2023-04-17
Started: 2022-05-15

Readme and manuals

Help Manual

Help pageTopics
SpliceWiz: efficient and precise alternative splicing analysis in RSpliceWiz-package SpliceWiz
Using Generalised linear models (GLMs) to analyse differential ASEs using edgeRaddPSI_edgeR ASE-GLM-edgeR fitASE_edgeR fitASE_edgeR_custom testASE_edgeR
Differential Alternative Splicing Event analysisASE-methods ASE_DESeq ASE_DoubleExpSeq ASE_edgeR ASE_edgeR_timeseries ASE_limma ASE_limma_timeseries
SpliceWiz filters to remove low-confidence alternative splicing and intron retention eventsASEFilter ASEFilter-class
Builds reference files used by SpliceWizBuild-Reference-methods buildFullRef buildRef getAvailableGO getNonPolyARef getResources
Collates a dataset from (processBAM) output files of individual samplescollateData
Converts genomic coordinates into a GRanges objectcoord2GR
Container to hold raw data for SpliceWiz coverage plotscovDataObject-class getCoverageData getGenomeData plotAnnoTrack showEvents showEvents,covDataObject-method
Calls SpliceWiz's C++ function to retrieve coverage from a COV fileCoverage getCoverage getCoverageBins getCoverageRegions getCoverage_DF
Container for plotly-based coverage plotscovPlotly-class getExonRanges getExonRanges,covPlotly-method setResolution setResolution,covPlotly-method showExons showExons,covPlotly-method
Versatile coverage plots for SpliceWizcondition condition,covPlotObject-method covPlotObject-class getPlotObject plotView tracks tracks,covPlotObject-method
SpliceWiz Example BAMs and NxtSE Experiment Objectexample-SpliceWiz-data SpliceWiz_example_bams SpliceWiz_example_NxtSE
Convenience Function to (recursively) find all files in a folder.findBAMS findFASTQ findSamples findSpliceWizOutput
Gene ontology (over-representation) analysis using enriched genes of top alternative splicing eventsextract_gene_ids_for_GO Gene-ontology-methods goASE goGenes plotGO subset_EventNames_by_GO
Launches the SpliceWiz Graphics User Interface (GUI) using Shiny DashboardGraphics-User-Interface GUI spliceWiz
Validates the given file as a valid COV fileisCOV
Construct data of percent-spliced-in (PSI) matrices and group-average PSIsmakeMatrix makeMeanPSI make_plot_data
Imports a collated dataset into the R session as an NxtSE objectmakeSE
Calculate low mappability genomic regionscalculateMappability generateSyntheticReads Mappability-methods
The NxtSE classcbind,NxtSE-method coerce,SummarizedExperiment,NxtSE-method covfile covfile,NxtSE-method covfile<- covfile<-,NxtSE-method down_exc down_exc,NxtSE-method down_exc<- down_exc<-,NxtSE-method down_inc down_inc,NxtSE-method down_inc<- down_inc<-,NxtSE-method junc_counts junc_counts,NxtSE-method junc_counts_uns junc_counts_uns,NxtSE-method junc_gr junc_gr,NxtSE-method junc_PSI junc_PSI,NxtSE-method NxtSE NxtSE-class NxtSE-methods rbind,NxtSE-method realize_NxtSE realize_NxtSE,NxtSE-method ref ref,NxtSE-method row_gr row_gr,NxtSE-method sampleQC sampleQC,NxtSE-method sampleQC<- sampleQC<-,NxtSE-method sourcePath sourcePath,NxtSE-method update_NxtSE update_NxtSE,NxtSE-method up_exc up_exc,NxtSE-method up_exc<- up_exc<-,NxtSE-method up_inc up_inc,NxtSE-method up_inc<- up_inc<-,NxtSE-method [,NxtSE,ANY,ANY,ANY-method [<-,NxtSE,ANY,ANY,NxtSE-method
RNA-seq Coverage Plots and Genome TracksplotCoverage plotGenome
Runs the OpenMP/C++ based SpliceWiz algorithmBAM2COV processBAM
Filtering for IR and Alternative Splicing EventsapplyFilters getDefaultFilters runFilter Run_SpliceWiz_Filters
Sets the number of threads used by SpliceWizsetSWthreads
STAR wrappers for building reference for STAR, and aligning RNA-sequencingSTAR-methods STAR_alignExperiment STAR_alignReads STAR_buildGenome STAR_buildRef STAR_loadGenomeGTF STAR_mappability STAR_version
ggplot2 themestheme_white theme_white_legend theme_white_legend_plot_track
View SpliceWiz Reference in read-able data framesView-Reference-methods viewASE viewExons viewGenes viewGO viewIntrons viewIR viewIR_NMD viewProteins viewTranscripts