Package: SpliceWiz 1.15.0
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:
SpliceWiz_1.15.0.tar.gz
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SpliceWiz_1.15.0.tgz(r-4.6-x86_64)SpliceWiz_1.15.0.tgz(r-4.6-arm64)SpliceWiz_1.15.0.tgz(r-4.5-x86_64)SpliceWiz_1.15.0.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
card.svg |card.png
SpliceWiz/json (API)
NEWS
| # Install 'SpliceWiz' in R: |
| install.packages('SpliceWiz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alexchwong/splicewiz/issues
On BioConductor:SpliceWiz-1.15.0(bioc 3.24)SpliceWiz-1.14.0(bioc 3.23)
softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp
Last updated from:37fa02b5b7. Checks:1 NOTE, 1 ERROR, 10 WARNING, 1 OK, 1 FAIL. Indexed: yes.
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| bioc-checks | NOTE | 309 | ||
| linux-devel-arm64 | ERROR | 677 | ||
| linux-devel-x86_64 | WARNING | 1014 | ||
| source / vignettes | OK | 651 | ||
| linux-release-arm64 | WARNING | 730 | ||
| linux-release-x86_64 | WARNING | 1069 | ||
| macos-release-arm64 | WARNING | 752 | ||
| macos-release-x86_64 | WARNING | 1203 | ||
| macos-oldrel-arm64 | WARNING | 1091 | ||
| macos-oldrel-x86_64 | WARNING | 1070 | ||
| windows-devel | WARNING | 929 | ||
| windows-release | WARNING | 1080 | ||
| windows-oldrel | WARNING | 804 | ||
| wasm-release | FAIL | 258 |
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:abindannotateAnnotationDbiAnnotationHubaskpassassertthatbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebslibcacachemcallrcigarillocliclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdendextenddigestdir.expirydplyrDTeggevaluateExperimentHubfarverfastmapfilelockfontawesomeforeachformatRfsfstfstcorefutile.loggerfutile.optionsgclusgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegridExtragtableh5mreadHDF5Arrayheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeNxtIRFdataompBAMopensslotelpatchworkpermutepheatmappillarpkgconfigplotlyplyrpngprettyunitsprocessxprogresspromisespspurrrqapR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppProgressRCurlregistryreshape2restfulrrhandsontablerhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoseriationshinyshinydashboardshinyFilesshinyWidgetssnowsourcetoolsSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTSPUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SpliceWiz: efficient and precise alternative splicing analysis in R | SpliceWiz-package SpliceWiz |
| Using Generalised linear models (GLMs) to analyse differential ASEs using edgeR | addPSI_edgeR ASE-GLM-edgeR fitASE_edgeR fitASE_edgeR_custom testASE_edgeR |
| Differential Alternative Splicing Event analysis | ASE-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 events | ASEFilter ASEFilter-class |
| Builds reference files used by SpliceWiz | Build-Reference-methods buildFullRef buildRef getAvailableGO getNonPolyARef getResources |
| Collates a dataset from (processBAM) output files of individual samples | collateData |
| Converts genomic coordinates into a GRanges object | coord2GR |
| Container to hold raw data for SpliceWiz coverage plots | covDataObject-class getCoverageData getGenomeData plotAnnoTrack showEvents showEvents,covDataObject-method |
| Calls SpliceWiz's C++ function to retrieve coverage from a COV file | Coverage getCoverage getCoverageBins getCoverageRegions getCoverage_DF |
| Container for plotly-based coverage plots | covPlotly-class getExonRanges getExonRanges,covPlotly-method setResolution setResolution,covPlotly-method showExons showExons,covPlotly-method |
| Versatile coverage plots for SpliceWiz | condition condition,covPlotObject-method covPlotObject-class getPlotObject plotView tracks tracks,covPlotObject-method |
| SpliceWiz Example BAMs and NxtSE Experiment Object | example-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 events | extract_gene_ids_for_GO Gene-ontology-methods goASE goGenes plotGO subset_EventNames_by_GO |
| Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard | Graphics-User-Interface GUI spliceWiz |
| Validates the given file as a valid COV file | isCOV |
| Construct data of percent-spliced-in (PSI) matrices and group-average PSIs | makeMatrix makeMeanPSI make_plot_data |
| Imports a collated dataset into the R session as an NxtSE object | makeSE |
| Calculate low mappability genomic regions | calculateMappability generateSyntheticReads Mappability-methods |
| The NxtSE class | cbind,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 Tracks | plotCoverage plotGenome |
| Runs the OpenMP/C++ based SpliceWiz algorithm | BAM2COV processBAM |
| Filtering for IR and Alternative Splicing Events | applyFilters getDefaultFilters runFilter Run_SpliceWiz_Filters |
| Sets the number of threads used by SpliceWiz | setSWthreads |
| STAR wrappers for building reference for STAR, and aligning RNA-sequencing | STAR-methods STAR_alignExperiment STAR_alignReads STAR_buildGenome STAR_buildRef STAR_loadGenomeGTF STAR_mappability STAR_version |
| ggplot2 themes | theme_white theme_white_legend theme_white_legend_plot_track |
| View SpliceWiz Reference in read-able data frames | View-Reference-methods viewASE viewExons viewGenes viewGO viewIntrons viewIR viewIR_NMD viewProteins viewTranscripts |