Alternative Splicing Tools A list of alternative splicing analysis resources
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Splice-aware mapping tools 2passtools: a tool for filtering long RNA-Seq alignment from minimap2 BFAST: a BLAT-like mapping tool. Only for SOLiD data. iMapSplice: a personalized RNA-Seq alignment tool PALMapper: a splice-aware mapping tool Rail-RNA: a cloud-enabled splice-aware mapping tool RUM: a splice-aware mapping tool SeqSaw: a splice-aware mapping tool Shark: mapping-free tool for fishing relevant reads in an RNA-Seq sample SpliceMap: a splice-aware mapping tool Subread: a splice-aware mapping tool featureCounts is a part of Subread to count features expression
STAR: a splice-aware mapping tool Alternative splicing and differential splicing detection tools ARH-Seq: a differential splicing detection tool The R code is in the supplementary materials
ASD: an alternative splicing event detection tool ASDT: an alternative splicing event detection tool ASGAL: an alternative splicing event detection tool ASpediaFI: identification of DAS events and co-regulated genes and pathways ASpli: an alternative splicing event and differential splicing detection tool ASprofile: an alternative splicing event detection tool ASTool: AS detection from plant RNA-Seq AStrap: an alternative splicing event prediction from transcript sequence CASH: a differential splicing analysis tool DARTS: an alternative splicing event detection tool DSGseq: a differential splicing detection tool EventPointer: an alternative splicing event detection tool FakIR: an intron retention identification tool FaRLine: a pipeline for alternative splicing event detection GESS: an exon skipping detection tool Based on not supporting tool MISO
iDiffIR: a differential intron retention tool iFLAS: a plant-optimized AS toolkit IntEREst: an intron retention identification tool iREAD: an intron retention identification tool IRFinder: an intron retention identification tool IRFinder is not maintained
jSplice: a differential splicing detection tool Not maintained.
JUM: an alternative splicing event detection tool Jutils/MntJULiP: A visualization toolkit for differential alternative splicing events/Now with covariates Keep Me Around: an intron retention identification tool KISSPLICE: an alternative splicing event detection tool KISSDE for differential splicing analysis
MAJIQ: an alternative splicing event detection tool nagnag: a nagnag splicing prediction tool PAVfinder: de novo isoforms inference from transcriptome assemblies Part of TAP pipeline
psichomics: an alternative splicing quantification and visualization tool PSI-Sigma: a differential splicing detection tool PTESFinder: a post-transcriptional exon shuffling rMATS: a differential splicing detection SAJR: a differential splicing tool SEASTAR: an alternative transcription start sites detection tool SGSeq: an alternative splicing event detection tool splAdder: an alternative splicing event detection tool SpliceDetector: an alternative splicing event detection tool spliceR: a tool for alternative splicing events, differential splicing detection, and isoform switching SpliceSeq: a tool for investigation of alternative mRNA splicing patterns in data from RNA-seq. SplicingCompass: a differential splicing tool SplicingTypesAnno: an alternative splicing event detection tool TECtool: a terminal codon characterization Whippet: an alternative splicing event detection tool Yanagi: a differential alternative splicing tool ACTOR: a latent Dirichlet model to compare expressed isoform proportions to a reference panel AERON: an isoform quantification and gene-fusion detection from long reads Alexa-Seq: an isoform qunification and differential isoform expression tool Not maintained.
BANDITS: a differential isoform usage BIISQ: an isoform inference tool BitSeq: an isoform quantification and differential isoform expression tool Cancer DEIso: a differential gene and isoform expression in cancer casper: an alternative splicing event detection tool CEM: a transcriptome assmbly and isoform quantification tool CIDANE: an isoform quantification and reconstruction tool Cufflinks: a suite of tools for an isoform quantification and differential isoform expression tool
Cufflinks assembles transcriptomes from RNA-Seq data and quantifies their expression.
Cuffcompare compares the assembled transcriptomes
Cuffmerge merges the tranacriptomes from multiple RNA-Seq libraries
Cuffquant computes the gene and transcript expression profiles
Cuffdiff compares expression levels of genes and transcripts in RNA-Seq
Cuffnorm normalizes the expression levels
URL PubMed GitHub
DiffSplice: a differential isoform expression detection tool DRIMseq: a differential isoform expression detection tool DTUrtle: a differential transcript usage for bulk and single-cell RNA-Seq EBseq: a differential isoform expression detection tool Event Analysis: an isoform inference (a conda recipe) SEVA: a differential isoform expression SEVA is implemented in the R package GSReg
HBA-DEALS: a differential gene and isoform expression iReckon: an isoform inference and quantification tool IsoEm2: an isoform quantification tool IsoformSwitchAnalyzer: an isoform switch detection The list of R scripts
IsoInfer: a tool for isoforms inference iso-kTSP: an isoform switch detection IsoSeq de novo: an isoform identification from IsoSeq The list of Python scripts
IsoSplitter: an isofrom quantification for long reads ISP: a tool for isoforms inference IUTA: a differential isoform expression tool kallisto: an isoform quantification tool sleuth is a differential isoform expression tool after kallisto analysis
metaDIEA: a differential isoform expression analysis MMSEQ: an isoform quantification tool MISO: a differential isoform expression tool Not maintained
MIETIE: an isoform inference and quantification tool mtim: an isoform inference tool NBBt-test: a versatile method for differential analysis of multiple types of RNA-seq data NBSplice: a differential isoform usage NLDMSeq: an isoform quantification tool NURD: an isoform quantification tool PennDiff: a differential isoform usage detection PRAM: transcript models inference from pooled RNA-seq PSGInfer: an isoforms inference and differential analysis tool rDiff: a differential isoform expression detection tool RSEM: an isoform quantification tool The variant of the tools is pRSEM: an isoform quantification with a complementary data
rSeqDiff: a differential isoform expression detection tool rSeqNP: a differential isoform expression detection tool Sailfish: an isoform quantification tool salmon: an isoform quantification tool SDEAP: a differential isoform expression detection tool for population data SLIDE: an isoform inference and quantification tool No documentation
SOSTAR: iSofOrmS annoTAtoR pipeline Sparselso: an isoform identification tool SpliceGrapher: a tool for creating splice graphs and isoforms predicting spliceR: a tool for alternative splicing, differential detection and isoform switching SplicingFactory: an isoform diversity StringTie: a transcriptome assembly and isoform quantification tool subgraphquant: a transcript abundance estimator SUPPA: an isoform quantification tool Archived
tappAS: a functional effect of alternative splicing TIGAR2: an isoform quantification tool from longer RNA-Seq TranD: transcript diversity metrics Traph: an isoform quantification tool TRIMD: Iso-Seq, RNA-Seq, and deepCAGE data integration for transcriptome resolution The list of Perl scripts
DEXSeq: a differential exon usage tool DIEGO: a differential alternative splicing tool DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization diffUTR: a differential exon usage analysis ExClust: a package for constitutive exons analysis Part of the sysSeq package. No easily accessible documentation
ExCluster: a differential exon expression tool FineSplice: a TopHat2 wrapper to identify expressed junctions FreePSI: an exon-inclusion ratio quantification tool HMMSplicer: a splice junctions detection HTSeq: an RNA-Seq quantification tool The tool can quantify exon expression
iGEMS: a model for alternative exon usage detection An R script
A list of scripts
iTAD: a switch-like exons identification The code is upon request
JunctionSeq: a differential exon and junctions usage LeafCutter: an intron quantification and differential analysis MISO: a differential isoform expression tool The tool also detects differentially regulated exons.
MISO also presents sashimi plots for exon expression visualisation.
No longer maintained.
PAIRADISE: a paired differential isoform expression Portcullis: a splice junctions detection Read-Split-Fly: a splice junctions detection (base on Read-Split-Walk and Read-Split-Run) RNAprof: a differential RNA processing tool SeqGSEA: a gene set enrichment analysis with differential expression and splicing SigFuge: a differential isoform expression detection tool SpliceJumper: a splice junctions detection SpliceLauncher: a splice junctions detection SPLICE-q: an intron splicing efficiency SpliceTrap: a tool to quantify exon inclusion levels using paired-end RNA-seq data Redirects to ESEfinder
SpliSER: a splice site usage quantification SplicingGraphs: a splicing graphs creation, visualization, and quantification tool Review 1
FIVEx: a eQTL and sQTL browser GLiMMPS: an sQTL detection
BioRxiv
The code will be after publication
PVAAS: a tool to identify SNVs associated with aberrant splicing SNPlice: variants that modulate Intron retention from RNA-sequencing data sQTLseekeR: an sQTL detection SplicePlot: an sQTL visualization No easily accessible documentation
ulfasQTL: an sQTL detection (based on sQTLseekeR) Splice sites prediction and cryptic splicing CADD-splice: a variant effect on alternative splicing CI-SpliceAI: machine learning predictions of disease causing splicing variants COSSMO: an alternative splicing site usage prediction The code for the model
CRYP-SKIP: an effect of exonic mutation CrypSplice: a cryptic splice variations prediction tool DASSI: splice identification from DNA sequences The model
DeepDSSR: a donor splice site recognition The model
Deep Splicing Code: an alternative splicing event prediction from sequence The code
DeltaSplice: splicing-altering mutations DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome EX-SKIP: a variant effect prediction on alternative splicing Exon ByPASS: predicting exon criticality GeneSplicer: a splice site prediction Genomic-Kmer-Surprisal-Model HAL: an effect of variants on alternative splicing Human Splicing Finder: a splice site prediction Limited access
MaxEntScan: a tool for human 5'splice sites scoring MMSplice: a tool for prediction of the effect of genetic variants on alternative splicing NetAspGene: a splice site prediction in Aspergillus NetGene2 Server: a splice site prediction NetUTR: a splice site prediction in 5'UTR regions of human genes NNSPLICE: a splice site prediction by neural network PEPSI: a prediction of PSI value changes due to genetic variants PredPSI-SVR: a prediction of PSI value changes due to genetic variants RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer rPGA: a hidden splicing variations SAVNet: a tool for detection of effect of genetic variants on alternative splicing SiLVA: prediction of synonymous (silent) mutations within the human genome SKIPPY: a tool for detection of exonic variants that modulate splicing Splice2Deep: a splice site prediction SpliceAI: a tool for detection of the effect of genetic variants on alternative splicing Spliceator: a splice site prediction Spliceman: a web tool for prediction of sequence variations in splicing SpliceView: a splice site prediction SpliceViNCI: a non-canonical splice sites prediction No code provided
SPANR: a splicing-based analysis of SNVs SQUIRLS: a tool that detects changes in splicing regulatory sequences TraP: transcript inferred pathogenecity score Alternative splicing regulation AGML: RBP-AS association prediction AIRBP: Identification of RNA-binding proteins using machine-learning techniques BPP: a branch point prediction branchpointer: a branch point prediction DeepRKE: prediction of RBP binding sites No documentation
DeeperBind (For DNA binding) DeepBtoD: RNA-binding proteins prediction via integrated deep learning dsRBPBind: the effect of RNA secondary structure on double-stranded RNA-protein binding dSreg: a differential splicing and regulation prediction ESEFinder: a web tool for exon splicing enhancers identification ExonScan: a regulatory exonic motifs identification The code is upon request
ExonSuite: a tool for PUF binding regions analysis The Python script with no documentation
LaBranchoR: a branchpoint prediction tool Last release: 2019, February, 20th
MIRA: a tool for mutation identification for RNA Alterations ModCon: a splice site usage modification tool No code
RBPmap: a tool for mapping binding sites of RNA binding proteins Last release: 2021, February
rMAPS2: a tool for RNA-binding protein analysis PCB: approach to infer the dynamic regulatory relationships between alternative splicing events RNABP: a branchpoint prediction Sparse Adjusted Motifs (SAM): modeling of RNA-binding protein motifs SPLASH2: a k-mer counting approach for regulated sequence variation detection SVM-BPfinder: a branchpoint prediction tool Last release: 2016
WDFSMF: an RNA-AS target prediction No documentation
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biosurfer: a computational approach for comparing protein isoforms jcast: takes in alternative splicing events and returns custom protein sequence databases for isoform analysis QUILTS: the identification of novel proteins, resulting from single nucleotide variants, splice variants, and fusion genes PASS: an alternative splicing detection from proteome pgdb and pypgatk: creation of proteogenomics databases based on ENSEMBL resources SpliceVista: a tool for splice variant identification and visualization in shotgun proteomics data SPLICIFY: a proteogenomic pipeline for differential splice variant identification TopPG: a proteogenomic tool for generating proteoform sequence databases with genetic alterations and alternative splicing events ALT-IN: predicting protein interaction network perturbation by alternative splicing CoSpliceNet: a co-splicing network tool DeepIII: an isoform-isoform interaction prediction DIGGER: a role of alternative splicing in protein-protein interactions DomainGraph: effect of alternative splicing on domain-domain interactions acorde: networks of isoform co-usage from single-cell data BRIE: an isoform quantification tool Expedition: an alternative splicing detection tool IsoCell: an approach for isoform-based single-cell clustering MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data Psix: splicing that changes across a landscape of single cells scAllele: detection and analysis of variants in scRNA-seq scASfind: Mining alternative splicing patterns in scRNA-seq SICILIAN: splice junctions identification in bulk and single RNA-Seq SingleSplice: an alternative splicing detection tool SpliZ: a splicing quantification score for single-cell Review 1
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ASAPA: a pipeline that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation A code is not found
brca-isoforms: long-read isoform analysis platform and sequencing resource for breast cancer CTAT-LR-fusion: fusion transcripts detection NAGATA: Nanopore guided annotation of transcriptome architectures deSALT: an alignment tool FLAME: a bioinformatics pipeline for alternative splicing analysis of gene-specific or transcriptome-wide long-read sequencing data Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing scallop-LR: a transcritome assembler SCASL: a single-cell clustering based on alternative splicing landscapes Isoform Function Inference/Functional interpretation ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events DeepIDA: isoform-disease associations prediction factR: Functional Annotation of Custom Transcriptomes IsoDA: an isoform-disease association prediction NMD Classifier: a nonsense mediated decay classifier n1pas: an alternatevely spliced pathway detection PathwaySplice: a pathway analysis for alternative splicing genes SAPFIR: A webserver for the identification of alternative protein features SpliceTools: a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing TS-Isofun: a tissue-specific isoform function prediction No code available
The code is not available
At-C-RNA: Arabidopsis thaliana CircRNAs Circ-LocNet: localisation prediction circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging DEBKS: A Tool to Detect Differentially Expressed Circular RNA FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence VirusCircBase: a database of virus circular RNAs LeafCutter: an intron quantification and differential analysis AIDD: a pipeline for transcript level analysis AltAnalyze: an alternative splicing event detection tool Kallisto-Splice is part of a tool for a splice-aware mapping
OneStopRNAseq: a pipeline for RNA-Seq analysis PPLine: a pipeline for SNP calling and gene/isoform quantification PipeOne-NM: RNA-Seq Analysis Pipeline for Non-Model Organisms RAP: a web pipeline for RNA-Seq analysis rmappet: a pipeline for alternative splicing analysis SeqCVIBE: Interactive Analysis, Exploration, and Visualization of RNA-Seq For RNA-Seq only
ACEScan: the algorithm for prediction of conserved alternatively spliced exons from pairs of conserved mouse/human exons The code is upon request
ASES: a tool for assessing the impact of alternative splicing, initiation and termination of transcription on protein diversity in evolution ASimulatoR: RNA-Seq reads with splicing simulation ASNEO: a detection of alternative splicing neoantigens BEERS2: RNA-Seq reads with splicing simulation CAMPAREE: an RNA expression simulator CHESSBOARD: Splicing-based subtyping EGIO: orthologous exons detection Last release
Enhanced Integrated Gradients: a method to identify specific features ERPIN: a mitochondrial intron detection eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping ESPRNN: epigenome-based splicing prediction Ex-Ex Primer: designing oligonucleotides spanning spliced nucleic acid regions ExOrthist: an exon evolution ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs FSOM: a methylation pattern associated with alternative splicing IsoDeconvMM: cell type deconvolution based on isoform composition IsoSel: an isoform phylogenetic analysis tool
Matt: feature extraction for alternative splicing
MBS: a genome browser annotation track for microRNA binding sites in the whole human transcriptome Mirage: multiple sequence isoform alignment MOCCASIN: a correction for confounders PIC-Me: a classification model between paralogs and isoforms RedRibbon: associations between gene and transcript level rnabridge-denovo: de novo Bridging Paired-end RNA-seq Data ORQAS: an alternative splicing quantification tool from RNA-Seq and Ribo-Seq PrimerSeq: a tool for RT-PCR primers design that evaluates alternative splicing events SCISSOR: a framework for identifying structural changes in RNA transcripts SimSpliceEvol: an alternative splicing-aware simulation of biological sequence evolution SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data SplicePie: an order of splicing prediction ThorAxe: an evolutionary splicing graphs construction TranscriptAchilles: a transcript-level biomarkers for cancer UNCOVER: the algorithm for predicting conserved alternatively spliced exons (and retained introns) in orthologous intron pairs (Upon request) AceView: a database of alternative splicing isoforms AltTrans: a database of alternative splicing and alternative polyadenilation (archived) APPRIS: a database of principal splice isoforms ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers AS-CMC: a pan-cancer database of alternative splicing for molecular classification of cancer ASpedia: a database of human alternative splicing ASPicDB: a database of alternative splicing patterns in human genes ASPN: a splicing-derived neoepitopes database CancerSplicingQTL: a database of SNPs that affect alternative splicing CanIsoNet: a database to study the functional impact of isoform switching events in diseases CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas CAS-viewer: a visualization tool of cancer alternatively splicing CuAS: a database of alternative splicing in cucumber dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs DBTSS: a database of transcription start sites eQTL Catalogue: a database of eQTL and sQTL ExonSkipAD: exon skipping in Alzheimer's disease ExonSkipDB: a functional characterization of skipped exons FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species FLIBase: a repository of full-length isoforms across human cancers and tissues Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels H-DBAS: a human alternative splicing database HEXEvent: a database of Human EXon splicing Events The Human Proteoform Atlas IDeAS: an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients IntroVerse: a comprehensive database of introns across human tissues ISOdb: a database of Iso-Seq isoforms ISOexpresso: a database of isoform expression in cancer Kassiopeia: a database of mutually exclusive exonomes LncAS2Cancer: alternative splicing in lncRNAs in cancer MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer MeDAS: a Metazoan Developmental Alternative Splicing database MutSpliceDB: A database of splice sites variants with RNA-seq based evidence on effects on splicing NMDtxDB: A database of NMD targets oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species Pan-cancer repository of validated natural and cryptic mRNA splicing mutations PerturbAtlas: an atlas of public genetic perturbation bulk RNA-seq datasets PID: Plant Intron Database PlaASDB: a comprehensive database of plant alternative splicing events in response to stress Plant Alternative Splicing Database PlantSPEAD: a splicing-related protein expression database PISE: Plant Intron-Splicing Efficiency Database PolyA_DB: a database of pre-mRNA cleavage and polyA sites ProSAS: a database of the effects of alternative splicing events on the structure of the resulting protein isoforms. RJunBase: a database of RNA splice junctions in human normal and cancerous tissues recount3: an online resource consisting of RNA-seq gene, exon, and exon-exon junction counts as well as coverage SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics S-CAP: a list of splice-related pathogenicity scores SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species SpliceAid: a database of experimentally proven RNA target motifs bound by splicing proteins in human scTEA-db: a database of novel terminal exon isoforms identified from human single cell transcriptomes TassDB: a tandem splice sites database TCGA SpliceSeq: splicing patterns alternation in TCGA TeaAS: a database of alternative splicing in tea plants Transposable element-derived alternative splicing in cancer TSVdb: TCGA splicing variants database VastDB: a database of alternative splicing profiles DoChaP: a domain-splicing visualization Geneapp: AS events visualization GFFView: a RNA-Seq viewer Integrated Genome Browser: a visual analysis of alternative splicing ggsashimi: an alternative splicing visualization Manananggal: a visualization of alternative splicing events PTMViz: Understanding PTM Cross Talk Through a Visualization Tool RNASeqViewer: a visualization tool for gene expression and isoforms ScisorWiz: visualizing differential isoform expression in single-cell long-read data SpliceV: a splicing visualization TraC: a visualization a shared between splice variants sequences VALERIE: visualizing splicing at single-cell Vials: a visualization of alternative splicing tool surfaltr: An R/Bioconductor package to benchmark surface protein isoforms by rapid prediction and visualization of transmembrane topologies BayesDenovo: a transcriptome assembly CLASS2: a transcriptome assembly tool ConSemble: a tool for trascriptome assembly improvement isoLASSO: a transcriptome assembly and isoform quantification tool Jumper: a transcriptome assembly tool MultiTrans: a transcriptome assembly Oases: a transcriptome assembly tool rnaSPAdes: a transcriptome assembly tool Roast: supertranscriptome assembly Scripture: a transcriptome assembly tool SOAPdenovo-trans: a transcriptome assembly tool Tiglon: a trascriptome assembly TRANS-Abyss: a transcriptome assembly tool TransRef: a transcriptome assembly Trinity: a transcriptome assembly tool Velvet: a transcriptome assembly tool TSIS: a time-series isoform switches detection tool