Package: IsoformSwitchAnalyzeR 2.7.0

Kristoffer Vitting-Seerup

IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

Authors:Kristoffer Vitting-Seerup [cre, aut], Jeroen Gilis [ctb]

# Install 'IsoformSwitchAnalyzeR' in R:

install.packages('IsoformSwitchAnalyzeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kvittingseerup/isoformswitchanalyzer/issues

Datasets:

exampleSwitchList - Example data for IsoformSwitchAnalyzeR
exampleSwitchListAnalyzed - Example data for IsoformSwitchAnalyzeR
exampleSwitchListIntermediary - Example data for IsoformSwitchAnalyzeR

On BioConductor:IsoformSwitchAnalyzeR-2.7.0(bioc 3.21)IsoformSwitchAnalyzeR-2.6.0(bioc 3.20)

geneexpression transcription alternativesplicing differentialexpression differentialsplicing visualization statisticalmethod transcriptomevariant biomedicalinformatics functionalgenomics systemsbiology transcriptomics rnaseq annotation functionalprediction geneprediction dataimport multiplecomparison batcheffect immunooncology

9.23 score 103 stars 122 scripts 593 downloads 16 mentions 50 exports 145 dependencies

Last updated 2 months agofrom:15ecc4e346. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 04 2024
R-4.5-win-x86_64	NOTE	Dec 04 2024
R-4.5-linux-x86_64	NOTE	Dec 04 2024
R-4.4-win-x86_64	NOTE	Dec 04 2024
R-4.4-mac-x86_64	NOTE	Dec 04 2024
R-4.4-mac-aarch64	NOTE	Dec 04 2024
R-4.3-win-x86_64	NOTE	Dec 04 2024
R-4.3-mac-x86_64	NOTE	Dec 04 2024
R-4.3-mac-aarch64	NOTE	Dec 04 2024

Exports:addORFfromGTF analyzeAlternativeSplicing analyzeCPAT analyzeCPC2 analyzeDeepLoc2 analyzeDeepTMHMM analyzeIntronRetention analyzeIUPred2A analyzeNetSurfP2 analyzeNovelIsoformORF analyzeORF analyzePFAM analyzeSignalP analyzeSwitchConsequences extractConsequenceEnrichment extractConsequenceEnrichmentComparison extractConsequenceGenomeWide extractConsequenceSummary extractGeneExpression extractGenomeWideAnalysis extractSequence extractSplicingEnrichment extractSplicingEnrichmentComparison extractSplicingGenomeWide extractSplicingSummary extractSubCellShifts extractSwitchOverlap extractSwitchSummary extractTopSwitches importCufflinksFiles importGTF importIsoformExpression importRdata importSalmonData isoformSwitchAnalysisCombined isoformSwitchAnalysisPart1 isoformSwitchAnalysisPart2 isoformSwitchTestDEXSeq isoformSwitchTestSatuRn isoformToGeneExp isoformToIsoformFraction preFilter prepareSalmonFileDataFrame subsetSwitchAnalyzeRlist switchPlot switchPlotGeneExp switchPlotIsoExp switchPlotIsoUsage switchPlotTopSwitches switchPlotTranscript

Dependencies:abind annotate AnnotationDbi AnnotationFilter AnnotationHub askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob boot BSgenome cachem cli clipr codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 DEXSeq digest dplyr edgeR ensembldb fansi farver fastmap filelock formatR futile.logger futile.options genefilter geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable hms httr httr2 hwriter IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle limma locfdr locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pbapply pfamAnalyzeR pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr pwalign R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors satuRn scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect txdbmaker tximeta tximport tzdb UCSC.utils utf8 vctrs VennDiagram viridisLite vroom withr XML xml2 xtable XVector yaml zlibbioc

IsoformSwitchAnalyzeR

Rendered fromIsoformSwitchAnalyzeR.Rmdusingknitr::rmarkdownon Dec 04 2024.

Last update: 2023-02-27
Started: 2017-04-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add CDS from a GTF file to a switchAnalyzeRlist.	addORFfromGTF
Analyse alternative splicing (including intron retention(s))	analyzeAlternativeSplicing analyzeIntronRetention
Import Result of External Sequence Analysis	analyzeCPAT
Import Result of External Sequence Analysis	analyzeCPC2
Import Result of DeepLoc2 Analysis	analyzeDeepLoc2
Import Result of a DeepTMHMM analysis	analyzeDeepTMHMM
Import Result of IUPred2A or IUPred3 analysis	analyzeIUPred2A
Import Result of NetSurfP2 analysis	analyzeNetSurfP2
Prediction of Isoform Open Reading Frames.	analyzeNovelIsoformORF
Prediction of Transcript Open Reading Frame.	analyzeORF
Import Result of PFAM analysis	analyzePFAM
Import Result of SignalP Analysis	analyzeSignalP
Analyze Consequences of Isoform Switches	analyzeSwitchConsequences
Create a switchAnalyzeRlist Object	createSwitchAnalyzeRlist switchAnalyzeRlist switchAnalyzeRlist-class
Example data for IsoformSwitchAnalyzeR	exampleSwitchList exampleSwitchListAnalyzed exampleSwitchListIntermediary
Analyze data for enrichment of specific consequences	extractConsequenceEnrichment
Compare enrichment of specific consequences between comparisons	extractConsequenceEnrichmentComparison
Genome wide Analysis of Consequences due to isoform switching	extractConsequenceGenomeWide extractGenomeWideAnalysis
Analyze Switch Consequences	extractConsequenceSummary
Extract raw gene counts or abundances from a switchAnalyzeRlist object.	extractGeneExpression
Extract nucloetide (and amino acid) sequence of transcripts.	extractSequence
Analyze data for enrichment of specific type of alternative splicing	extractSplicingEnrichment
Compare enrichment of specific type of alternative splicing between comparisons	extractSplicingEnrichmentComparison
Genome wide Analysis of alternative splicing	extractSplicingGenomeWide
Extracts alternative splicing summary	extractSplicingSummary
Global overview of sub-cellular location changes	extractSubCellShifts
Visualize Switch Overlap	extractSwitchOverlap
Summarize Isoform Switches test Result.	extractSwitchSummary
Extract Top Isoform Switches.	extractTopSwitches
Import CuffDiff (Cufflinks) Data Into R	importCufflinksFiles
Import Transcripts from a GTF file into R	importGTF
Import expression data from Kallisto, Salmon, RSEM or StringTie into R.	importIsoformExpression
Create SwitchAnalyzeRlist From Standard R Objects	importRdata
Direct creation of a switchAnalyzeRlist from Salmon quantification	importSalmonData
Isoform Switch Analysis Workflow: Extract, Annotate and Visualize all Significant Isoform Switches	isoformSwitchAnalysisCombined
Isoform Switch Analysis Workflow Part 1: Extract Isoform Switches and Their Bio-sequences	isoformSwitchAnalysisPart1
Isoform Switch Analysis Workflow Part 2: Plot All Isoform Switches and Their Annotation	isoformSwitchAnalysisPart2
Statistical Test for identifying Isoform Switching via DEXSeq	isoformSwitchTestDEXSeq
Statistical Test for identifying Isoform Switching via satuRn.	isoformSwitchTestSatuRn
Sum transcript/isoform expression to gene get level expression.	isoformToGeneExp
Calculate isoform fraction from isoform abundance matrix	isoformToIsoformFraction
Filtering of a switchAnalyzeRlist	preFilter
Prepare data.frame needed run importSalmonData.	prepareSalmonFileDataFrame
A function which subset all entries in a switchAnalyzeRlist.	subsetSwitchAnalyzeRlist
Isoform Switch Analysis Plot	switchPlot
Plots for Analyzing Expression and Isoform Usage	switchPlotGeneExp switchPlotIsoExp switchPlotIsoUsage
Creating the Isoform Switch Analysis Plot for the Top Switches	switchPlotTopSwitches
Plot Transcript Structure and Annotation	switchPlotTranscript