IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Bioconductor version: 3.23 · Package version: 2.12.0
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 RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IsoformSwitchAnalyzeR")Details
| Maintainer | Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com> |
| Author | Kristoffer Vitting-Seerup [cre, aut] (ORCID: <https://orcid.org/0000-0002-6450-0608>), Chunxu Han [ctb], Jeroen Gilis [ctb] (ORCID: <https://orcid.org/0000-0001-8415-0943>), Elena Iriondo Delgado [ctb] |
| License | GPL (>= 2) |
| URL | http://bioconductor.org/packages/IsoformSwitchAnalyzeR/ |
| Bug Reports | https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues |
| Downloads rank | 729 |
| Source branch | RELEASE_3_23 |
| biocViews | AlternativeSplicing, Annotation, BatchEffect, BiomedicalInformatics, DataImport, DifferentialExpression, DifferentialSplicing, FunctionalGenomics, FunctionalPrediction, GeneExpression, GenePrediction, ImmunoOncology, MultipleComparison, RNASeq, Software, StatisticalMethod, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics, Visualization |
Documentation
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Dependencies
Depends: R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR
Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, Seqinfo, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment, tidyr, S4Vectors, BiocParallel, pwalign
Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown