/Alternative-Splicing-Tools

A list of alternative splicing analysis resources

Alternative Splicing Tools

A list of alternative splicing analysis resources

Splice-aware mapping tools

2passtools: a filtered realignment

BBMap

Last release: 2021, February, 3rd

BFAST: a BLAT-like mapping tool

Last release: 2011, October, 29th

ContextMap2

Last release: not found

CRAC

Last release: 2016, January, 29th

DART

Last release: 2019, May, 7th

ExceS-A

GSNAP

Last release: 2021, February, 22nd

HISAT2

Last release: 2020, July, 24th

iMapSplice: a personalized RNA-Seq alignment tool

Last release: 2019, February, 8th

Magic-BLAST

Last release: 2021, March

MapSplice3

Last release: 2019, May, 30th (the last commit)

minimap2

Last release: 2019, May, 5th

PALMapper: a splice-aware mapping tool

Last release: 2013, July, 2013

Rail-RNA: a cloud-enabled splice-aware mapping tool

Last release:

RUM: a splice-aware mapping tool

Last release: 2015, January, 27th

Scipio: a BLAT-based alignment tool to determine the gene structure given a protein sequence and a genome sequence

Last release: 2013, May, 24th

segemehl

Last release: 2018, December, 25th

SeqSaw: a splice-aware mapping tool

Last release: 2011, August, 10th

SpliceFamAlign: a CDS-to-gene alignment

Last release: 2018, August, 6th (the last commit)

SpliceMap: a splice-aware mapping tool

Last release: 2010, October, 23rd

Subread: a splice-aware mapping tool

Last release: 2020, May, 13th

featureCounts is a part of Subread to count features expression

STAR: a splice-aware mapping tool

Last release: 2021, February, 20th

UnSplicer: a splice-aware alignment and junction detection tool

Last release: 2013, November, 25th

Alternative splicing and differential splicing detection tools

Event-level

AltAnalyze: an alternative splicing event detection tool

Kallisto-Splice is a part of a tool for a splice-aware mapping

Last release: 2021, January, 14th

ARH-Seq: a differential splicing detection tool

Last release: 2014

The R code is in the supplementary materials

ASDT: an alternative splicing event detection tool

Last release: 2018, April, 17th

ASGAL: an alternative splicing event detection tool

Last release: 2020, June, 22nd

ASpediaFI: identification of DAS events and co-regulated genes and pathways

AS-Quant

ASpli: an alternative splicing event and differential splicing detection tool

Last release: 2017, February, 25th

ASprofile: an alternative splicing event detection tool

Last release:

AStrap: an alternative splicing event prediction from transcript sequence

Last release: 2020, November, 13th

CASH: a differential splicing analysis tool

Last release: 2018, April, 3rd

CATANA: an alternative splicing annotation

Last release: 2018, November, 28th

casper: an alternative splicing event detection tool

Last release: not found

COSSMO: an alternative splicing site usage prediction

Last release: 2018, July, 4th (the last commit)

DARTS: an alternative splicing event detection tool

Last release: 2019, February, 26th

Deep Splicing Code: an alternative splicing event prediction from sequence

Last release: 2020, September, 5th (the last commit)

DIEGO: a differential alternative splicing tool

Last release: 2019, December, 3rd

DSGseq: a differential splicing detection tool

Last release: 2012, May, 14th

EventPointer: an alternative splicing event detection tool

Last release: not found

FakIR: an intron retention identification tool

Last release: 2021, January, 28th (the last commit)

FARLINE: a pipeline for alternative splicing event detection

Last release: not found

GESS: an exon skipping detection tool

Last release: not found

iDiffIR: a differential intron retention tool

Last release: 2015

IntEREst: an intron retention identification tool

Last release: not found

iREAD: an intron retention identification tool

Last release: 2021, February, 16th

IRFinder: an intron retention identification tool

Last release: 2020, August, 27th

IsoSplitter

Last release:

jSplice: a differential splicing detection tool

Last release: 2017, July, 4th. Not maintained.

JUM: an alternative splicing event detection tool

Last release: 2019, July, 2019

Keep Me Around: an intron retention identification tool

Last release: 2019, January, 30th (the last commit)

KISSPLICE: an alternative splicing event detection tool

KISSDE for differential splicing analysis Last release: 2020, July, 2nd

MAJIQ: an alternative splicing event detection tool

Last release: not found

Manananggal: a visualization of alternative splicing events

Last release: 2016, December, 8th (the last commit)

nagnag: a nagnag splicing prediction tool

Last release: 2015, August, 4th

psichomics: an alternative splicing quantification and visualization tool

Last release: not found

PSI-Sigma: a differential splicing detection tool

Last release: 2021, February, 16th

PTESFinder: a post-transcriptional exon shuffling

Last release: 2019, September, 4th

rMATS: a differential splicing detection

Last release: 2021, February, 8th

RNAprof: a differential RNA processing tool

Last release: 2017, May, 24th

SAJR: a differential splicing tool

Last release: not found

SeqGSEA: a gene set enrichment analysis with differential expression and splicing

Last release: 2018, December, 12th (the last commit)

SGSeq: an alternative splicing event detection tool

Last release:not found

splAdder: an alternative splicing event detection tool

Last release: 2019, November, 19th

Spliceator: a splice site prediction

SpliceDetector: an alternative splicing event detection tool

Last release: not found

SplicePie: an order of splicing prediction

Last release: 2015, February, 20th (the last commit)

spliceR: a tool for alternative splicing events, differential splicing detection and isoform switching

Last release:_ not found_. Published in 2014

SpliceSeq: a tool for investigation of alternative mRNA splicing patterns in data from RNA-seq.

The tool detects events, compares between samples and predicts the consequence on a protein structure

Last release: 2014, February, 21st

SplicingCompass: a differential splicing tool

Last release: 2019, October, 24th (the last commit)

SplicingTypesAnno: a alternative splicing event detection tool

Last release: 2015, July, 31st

SpliSER: a splice site strength quantification

SUVA

Last release

Vials: a visualization of alternative splicing tool

Last release: 2017, February, 7th

Webscipio: a web tool for prediction of eukaryotic gene structures

Last release:

Whippet: an alternative splicing event detection tool

Last release: 2021, March

Yanagi: a differential alternative splicing tool

Last release: 2019, November, 27th

Isoform-level

ACTOR: a latent Dirichlet model to compare expressed isoform proportions to a reference panel

Last release:

AERON: an isoform quantification and gene-fusion detection from long reads

Last release: 2020, November, 23rd (the last commit)

Alexa-Seq: an isoform qunification and differential isoform expression tool

Last release: not found. Not maintained.

AstaFunk: an alternatively spliced domains detection

Last release: not found

Augustus: an isoform inference tool

Last release: 2020, December, 11th

BANDITS: a differential isoform usage

Last release: not found

BayesDenovo: a transcriptome assembley

Last release:

BIISQ: an isoform inference tool

Last release: 2017, March, 19th

BitSeq: an isoform quantification and differential isoform expression tool

Last release: 2019, August, 12th (the last commit cjBitSeq)

Cancer DEIso: a differential gene and isoform expression in cancer

Laste release:

CAS-viewer: a visualization tool of cancer alternatively splicing

Last release: 2017

CEM: a transcriptome assmbly and isoform quantification tool

Last release: 2012, November, 17th

CIDANE: an isoform quantification and reconstruction tool

Last release: 2019, February, 12th

CLASS2: a transcriptome assembly tool

Last release: 2017, May, 17th

ConSemble: a tool for trascriptome assembly improvement

Last release:

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 Last release: 2016, July, 1st
  • URL
  • PubMed
  • GitHub

DiffSplice: a differential isoform expression detection tool

Last release: 2013, January, 1st

DRIMseq: a differential isoform expression detection tool

Last release: 2017, December, 20th (the last commit of BayesDRIMSeq)

DTUrtle: a differential transcript usage for bulk and single-cell RNA-Seq

Last release

EBseq: a differential isoform expression detection tool

Last release:_ not found_

Event Analysis: an isoform inference (a conda recipe)

Last release: 2019, April, 9th

FineSplice: a TopHat2 wrapper to identify expressed juntions

Last release: 2014, April, 1st

GFFView: a RNA-Seq viewer

Last release: not found

Graph Salmon: a transcript abundance quantification

Last release:

GSReg: a differential isoform expression

Last release: not found

HBA-DEALS: a differential gene and isoform expression

Last release: 2020, May, 11th

Integrated Genome Browser: a visual analysis of alternative splicing

Last release: 2020, December, 3rd

iReckon: an isoform inference and quantification tool

Last release: not found

IsoEm2: an isoform quantification tool

Last release: 2017, April, 3rd

IsoformSwitchAnalyzer: an isoform switch detection

Last release: not found

IsoformUsage

IsoInfer: a tool for isoforms inference

Last release: 2010, September, 9th

iso-kTSP: an isoform switch detection

Last release: 2015, May, 5th (the last commit)

isoLASSO: a transcriptome assembly and isoform quantification tool

Last release: 2012, November, 17th

IsoSeq de novo: an isoform identification from IsoSeq (Python scripts)

Last release: 2017, September, 14th

ISP: a tool for isoforms inference

Last release: 2014, October, 15th

IUTA: a differential isoform expression tool

Last release:_ not found_. Published in 2014.

Jumper: a transcriptome assembly tool

kallisto: an isoform quantification tool

sleuth is a differential isoform expression tool after kallisto analysis

Last release: 2020, February, 13th

metaDIEA: a differential isoform expression analysis

Last release

MMSEQ: an isoform quantification tool

Last release: 2019, November, 11th

MISO: a differential isoform expression tool

Last release: 2019, May, 17th. No longer maintained.

MIETIE: an isoform inference and quantification tool

Last release: 2016, March, 18th

MINTIE

Last release:

mtim: an isoform inference tool

Last release: 2013, April, 18th

MultiTrans: a transcriptome assembly

Last release

NBSplice: a differential isoform usage

Last release: not found

NLDMSeq: an isoform quantification tool

Last release: 2016, June, 27th (the last commit)

NURD: an isoform quantification tool

Last release: not found. Published in 2013.

Oases: a transcriptome assembly tool

Last release: 2011, December, 6th

PAIRADISE: a paired differential isoform expression

Last release: 2020, June, 9th

PAVfinder: de novo isoforms inference from transcriptome assemblies

Last release: 2020, December, 28th

PennDiff: a differential isoform usage detection

Last release: 2020, December, 20th

PRAM: transcript models inference from pooled RNA-seq

Last release: not found

PSGInfer: an isoforms inference and differential analysis tool

Last release: 2013, October, 25th

QuickIsoSeq

RNASeqViewer: a visualization tool for gene expression and isoforms

Last release: 2013, October, 14th

rnaSPAdes: a transcriptome assembly tool

Last release: 2021, February

rDiff: a differential isoform expression detection tool

Last release: 2020, June, 19th (the last commit)

RSEM: an isoform quantification tool

The variant of the tools is pRSEM: an isoform quantification from a complementary data Last release: 2020, February, 14th

rSeqDiff: a differential isoform expression detection tool

Last release: not found. Published in 2013

rSeqNP: a differential isoform expression detection tool

Last release:

Sailfish: an isoform quantification tool

Last release: 2016, April, 14th

salmon: an isoform quantification tool

Last release: 2020, November, 26th

SDEAP: a differential isoform expression detection tool for population data

Last release: 2017, March, 15th (the last commit)

Scripture: a transcriptome assembly tool

Last release:

SigFuge: a differential isoform expression detection tool

Last release:_ not found_. Published in 2014.

SLIDE: an isoform inference and quantification tool

Last release: 2012, May, 17th

SOAPdenovo-trans: a transcriptome assembly tool

Last release: 2017, August, 23rd

Sparselso: an isoform identification tool

Last release: 2017, October, 11th

SpliceGrapher: a tool for creating splice graphs and isoforms predicting

Last release: 2014, April, 24th

spliceR: a tool for alternative splicing, differential detection and isoform switching

Last release:_ not found_. Published in 2014

SplicingFactory: an isoform diversity

Last release:

StringTie: a transcriptome assembly and isoform quantification tool

Last release: 2021, March, 4th

subgraphquant: a transcript abundance estimator

SUPPA: an isoform quantification tool

Last release: 2018, February, 22nd

tappAS: a functional effect of alternative splicing

Last release: 2021, January, 8th

TIGAR2: an isoform quantification tool from longer RNA-Seq

Last release: 2015, February, 19th

Tiglon: a trascriptome assembly

TRANS-Abyss: a transcriptome assembly tool

Last release: 2018, February, 19th

TransRef: a transcriptome assembly

Last release

Traph: an isoform quantification tool

Last release: 2014, September, 2nd

TRIMD: Iso-Seq, RNA-Seq and deepCAGE data integration for transcriptome resolution (Perl scripts)

Last release: 2020, September, 9th (the last commit)

Trinity: a transcriptome assembly tool

Last release: 2015, January, 24th

TSIS: a time-series isoform switches detection tool

Last release: 2018, December, 29th (the last commit)

Velvet: a transcriptome assembly tool

Last release: 2018, July, 5th

Exon-level

ChopStitch: an exon identification and splice graph construction out of transcriptome assembly and WGS

Last release: 2018, November, 8th

DEXSeq: a differential exon usage tool

diffUTR: a differential exon usage analysis

ExClust: a package for constitutive exons analysis

Part of the sysSeq package.

Last release: 2015, July, 17th (the last commit)

ExCluster: a differential exon expression tool

Last release: not found. Published in 2020.

FreePSI: an exon-inclusion ratio quantification tool

Last release: 2017, September, 5th

ggsashimi: an alternative splicing visualization

Last release: 2021, February, 10th

HMMSplicer: a splice junctions detection

Last release: 2010, November, 25th

HTSeq: a RNA-Seq quantification tool

The tool can quantify exon expression

Last release: 2020, April, 18th

iGEMS: a model for alternative exon usage detection (R scripts)

Last release: 2016, April, 13th

IntEREst: an intron retention estimation tool

Last release: not found

Intron-Essentiality

iTAD: a switch-like exons identification (Upon request)

Last release: not found

JunctionSeq: a differential exon and junctions usage

Last release: not found

LeafCutter: an intron quantification and differential analysis

Last release: 2017, September, 26th

MicroExonator

MISO: a differential isoform expression tool

The tool also detects differentially regulated exons. MISO also presents sashimi plots for exon expression visualisation.

Last release: 2019, May, 17th. No longer maintained.

Portcullis: a splice junctions detection

Last release: 2018, March, 19th

Read-Split-Fly: a splice junctions detection (base on Read-Split-Walk and Read-Split-Run)

Last release: 2016, January, 6th

SpliceJumper: a splice junctions detection

Last release: 2015, June, 29th (the last commit)

SpliceLauncher: a splice junctions detection

Last release: 2021, February, 15th

SPLICE-q: an intron splicing efficiency

Last release:

SpliceTrap: a tool to quantify exon inclusion levels using paired-end RNA-seq data

Last release: 2013, May, 17th

SpliceV: a splicing visualization

Last release: 2019, September, 27th (the last commit)

SplicingGraphs: a splicing graphs creation, visualization and quantification tool

Last release: 2020, November, 3rd

TECtool: a terminal codon characterization

Last release: 2018, June, 22th

sQTL analysis

FIVEx: a eQTL and sQTL browser

Last release:

GLiMMPS: an sQTL detection

Last release: 2013, March, 12th

PVAAS: a tool to identify SNVs associated with aberrant splicing

Last release:

sQTLseekeR: an sQTL detection

Last release: 2015, June, 29th

SplicePlot: an sQTL visualization

Last release: 2013, October, 15th

ulfasQTL: an sQTL detection (based on sQTLseekeR)

Last release: not found

Splice sites prediction and variations analysis

CADD-splice: a a varian effect on alternative splicing

CRYP-SKIP: an effect of exonic mutation

Laste release: 2008

CrypSplice: a cryptic splice variations prediction tool

Last release:

DASSI: splice identification from DNA sequences

DeepDSSR: a donor splice site recognition (a model)

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

EBChangePoint: a splice site prediction tool

Last release: 2015, May

EX-SKIP: a variant effect prediction on alternative splicing

Last release: 2010

GeneSplicer: a splice site prediction

Last release:_ not found_

HAL: an effect od variants on alternative splicing

Last release: not found

Human Splicing Finder: a splice site prediction (free limited access)

Last release:_ not found_

IntSplice2

Last release:

KipoiSplice

Laste release

MaxEntScan: a tool for human 5'splice sites scoring

Last release:_ not found_

McSplicer

MIRA: a tool for mutation identification for RNA Alterations

Last release: 2018, July, 3rd

MMSplice: a tool for prediction of effect of genetic variants on alternative splicing

Last release: 2021, February, 20th

MTSplice

ModCon: a splice site usage modification tool

Last release:

MutationTaster2021

Laste release:

NetAspGene: a splice site prediction in Aspergillus

Last release:_ not found_

NetGene2 Server: a splice site prediction

Last release: 2017, May, 30th

NetUTR: a splice site presiction in 5'UTR regions of human genes

Last release: _ not found_

NNSPLICE: a splice site prediction by neural network

Last release: 1997, January

PEPSI: a prediction of PSI value changes due to genetic variants

Last release: 2019, May, 15th

PredPSI-SVR: a prediction of PSI value changes due to genetic variants

Last release: 2020, July, 10th

regSNP-intron: a tool which predicts disease-causing probability of human intronic single nucleotide variants (iSNVs)

Last release: 2019, September, 27th

rPGA: a hidden splicing variations

Last release: 2016, June, 24th (the last commit)

SAVNet: a tool for detection of effect of genetic variants on alternative splicing

Last release: 2019, May, 18th

S-CAP

Last release:

SiLVA: prediction of synonymous (silent) mutations within the human genome

Last release: 2013, July, 12th

SKIPPY: a tool for detection of exonic variants that modulate splicing

Last release: 2011, March, 2nd

SPIDEX

Last release

Splice2Deep: a splice site prediction

Last release: 2019, August, 7th

SpliceAI: a tool for detection of effect of genetic variants on alternative splicing

Last release: 2020, March, 7th

Spliceman: a web tool for predition of sequence variations in splicing

Last release:

SpliceView: a splice site prediction

Last release: not found

SpliceViNCI: a non-canonical splice sites prediction

Laste release:

SPANR: a splicing-based analysis of SNVs

Last release:

SQUIRLS: a tool that detects changes in splicing regulatory sequences

Last release:

TraP: transcript inferred pathogenecity score

Last release

Alternative splicing regulation

AIRBP: Identification of RNA-binding proteins using machine learning techniques

BPP: a branch point prediction

Last release: 2017, May, 22nd (the last commit)

branchpointer: a branch point prediction

Last release: not found

DeepRKE: prediction of RBP binding sites

dsRBPBind: the effect of RNA secondary structure on double stranded RNA-protein binding

dSreg: a differential splicing and regulation prediction

Last release: 2019 August 7th

ESEFinder: a web tool for exon splicing enhancers identification

Last release: not found

ExonScan: a regulatory exonic motifs identitfication (Upon request)

Last release: not found

ExonSuite: a tool for PUF binding regions analysis

Last release: 2013, January, 13th (the last commit)

LaBranchoR: a branchpoints prediction tool

Last release: 2019, February, 20th

RBPmap: a tool for mapping binding sites of RNA binding proteins

Last release: 2021, February

rMAPS2: a tool for RNA-binding protein analysis

Last release: 2020, March, 20th

RNABP: a branchpoint prediction

Last release: 2020

SVM-BPfinder: a branchpoints prediction tool

Last release: 2016

WDFSMF: an RNA-AS target prediction

Last release:

Proteomics

jcast: takes in alternative splicing events and returns custom protein sequence databases for isoform analysis

Last release: March, 2021 (the last commit)

Long-Read-Proteogenomics

pgdb and pypgatk: creation of proteogenomics databases based on ENSEMBL resources

QUILTS: the identification of novel proteins, resulting from single nucleotide variants, splice variants and fusion genes

Last release: not found

PASS: an alternative splicing detection from proteome

Last release: 2019, April, 29th

SpliceVista: a tool for splice variant identification and visualization in shotgun proteomics data

Last release: 2017, June 21st (the last commit)

SPLICIFY: a proteogenomic pipeline for differential splice variant identification

Last release: 2018, May, 28th

TopPG: a proteogenomic tool for generating proteoform sequence databases with genetic alterations and alternative splicing events

Network analysis

ALT-IN: predicting protein interaction network perturbation by alternative splicing

CoSpliceNet: a co-splicing network tool

Last release: 2017, October, 18th (the last commit)

DeepIII: an isoform-isoform interaction prediction

DIGGER: a role of alternative splicing in protein-protein interactions

Last release: not found

DomainGraph: effect of alternative splicing on domain-domain interactions

Last release: December, 2018

n1pas: a alternatevely spliced pathway detection

Last release: 2019, April, 3rd

PathwaySplice: a pathway analysis for alternative splicing genes

Last release: not found

Single cell data

BRIE: an isoform quantification tool

Last release: 2018, June, 3rd

DTUrtle: a differential transcript usage for bulk and single-cell RNA-Seq

Last release

Expedition: an alternative splicing detection tool

Last release:

IsoCell: an approach for isoform-based single cell clustering

SICILIAN: splice junctions identfication in bulk and single RNA-Seq

Last release

SingleSplice: an alternative splicing detection tool

Last release: 2016, July, 7th (the last commit)

VALERIE: visualising splicing at single-cell

Last release: not found

Long reads

BRCA-LRseq-pipeline

deSALT: an alignment tool

Last release: 2020, August, 20th

flair

Last release: 2020, May, 4th

FLAME: a bioinformatics pipeline for alternative splicing analysis of gene-specific or transcriptome-wide long-read sequencing data

Last release:

LIQA

Last release:

scallop-LR: a transcritome assembler

Last release: 2020, May, 22nd

SpliceHunter

Last release: 2017, March, 23rd

TALON

uLTRA

Last release:

Isoform Function Prediction

DeepIDA: isoform-disease associations prediction

DeepIsoFun

Last release:

DIFFUSE

Last release: 2020, October, 29th

DMIL-IsoFun

Last release:

IsoDA: an isoform-disease association prediction

Last release:

Iso-Net

IsoResolve

NMD Classifier: a nonsense mediated decay classifier

Last release: 2019, April, 11th

TRIFID

TS-Isofun: a tissue-specific isoform function prediction

Last release

Circular RNA

Review 1

AQUARIUM

Last release:

CircAST

Last release: 2020, February, 26th

Circall

Last release

CIRCExplorer

CircIMPACT

Last release

CirComPara2

Last release:

CircSplice

Last release: 2019, February, 27th

Ciri

Last release: 2021, March, 15th

DEBKS: A Tool to Detect Differentially Expressed Circular RNA

DMC-CDA

find_circ

FUCHS

Last release: 2020, August, 17th

JEDI

PCirc

psirc

SRCP

Last release

Aberrant Splicing

Bisbee

Last release

FRASER

Other

3D RNA-Seq: a pipeline

ACEScan: the algorithm for prediction of conserved alternatively spliced exons from pairs of conserved mouse/human exons (Upon request)

Last release: 2005, July, 10th

AIDD: a pipeline for transcript level analysis

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

Last release: 2020, December, 16th

ASNEO: a detection of alternative splicing neoantigens

Last release: 2020, May, 24th

BEERS: RNA-Seq reads with splicing simulation

Last release: 2015, December, 9th (the last commit)

CAMPAREE: an RNA expression simulator

Last release

Enhanced Integrated Gradients: a method to identify specific features

Last release: 2020, June, 30th

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

Last release:

ESPRNN: epigenome-based splicing prediction

Last release: 2020, February, 11th

Ex-Ex Primer: designing oligonucleotides spanning spliced nucleic acid regions

Exon ByPASS: predicting exon criticality

ExOrthist: an exon evolution

ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs

FSOM: a methylation patterns associated with alternative splicing

Last release: 2015, September, 3rd

Genomic-Kmer-Surprisal-Model

IsoDeconvMM: cell type deconvolution based on isoform composition

IsoSel: an isoform phylogenetic analysis tool

Last release: not found

Matt: a down-stream alternative splicing analysis

Last release: 2019, May, 27th

Mirage: multiple sequence isoform alignment

Last release: 2021, January, 21st

MOCCASIN: a correction for confounders

OneStopRNAseq: a pipeline for RNA-Seq analysis

Includes rMATS and DEXSeq Last release: not found

PIC-Me: a classification model between paralogs and isoforms

Last release:

RAP: a web pipeline for RNA-Seq analysis

Reboot:

Last release

ORQAS: an alternative splicing quantification tool from RNA-Seq and Ribo-Seq

Last release: 2020, April, 23rd

PPLine: a pipeline for SNP calling and gene/isoform quantification

Last release: 2018, March, 26th

PrimerSeq: a tool for RT-PCR primers design that evaluate alternative splicing events

Last release: 2016, November, 18th

SCISSOR: a framework for identifying structural changes in RNA transcripts

SEASTAR: an alternative transcription start sites detection tool

Last release: 2017, October, 26th

SimSpliceEvol: an alternative splicing-aware simulation of biological sequence evolution

Last release: 2019, august, 2nd

Shark: mapping-free tool for fishing relevant reads in an RNA-Seq sample

Last release: 2020, July, 6th

SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

SpliZ: a splicing quantification score

ThorAxe: an evolutionary splicing graphs construction

Last release:

TraC: a shared between splice variants sequences

Last release: 2018, May, 24th

TranscriptAchilles: a transcript-level biomarkers for cancer

Last release: 2019

Transposable element-derived alternative splicing in cancer

Last release: not found

UNCOVER: the algorithm for predicting conserved alternatively spliced exons (and retained introns) in orthologous intron pairs (Upon request)

Last release: not found

Databases

AceView: a database of alternative splicing isoforms

Last update: 2012, October, 16th

Organisms: human, mouse, rat, worm, arabidopsis

AltTrans: a database of alternative splicing and alternative polyadenilation (archived)

Last update: 2008, September, 5th

Organisms: human, mouse, rat

APPRIS: a database of principal splice isoforms

Last update: 2021

Organisims: 19 vertebrate and invertebrate genomes

Arabidopsis PeptideAtlas

Last update

ASCOT

Last update

ASlive: a database for alternative splicing in livestock animals

Last update: 2019, June, 25th

Organisms: cattle, sheep, pig, chicken, horse

ASpedia: a database of human alternative splicing

Last update: 2017, June, 30th

Organisims: human

ASPicDB: a database of alternative splicing patterns in human genes

Last update: 2017, May, 4th, 196,446 splicing events

Organism: human

ASPN: a splicing-derived neoepitopes database

Last update:

At-C-RNA: Arabidopsis thaliana CircRNAs

Blood Proteoform Atlas

CancerSplicingQTL: a database of SNPs that affect alternative splicing

Last update: 2021

Organism: human

CuAS: a database of alternative splicing in cucumber

Last update: 2021

Organism: 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

Last update: 2017, December, 21st

Organism: human

eQTL Catalogue: a database of eQTL and sQTL

Last update:

ExonSkipAD: exon skipping in Alzheimer's disease

Last update:

ExonSkipDB: a functional characterization of skipped exons

Last update: not found

Organism: Human

GreenCircRNA

H-DBAS: a human alternative splicing database

Last update: 2011, December, 26th

Organism: human

HEXEvent: a database of Human EXon splicing Events

Last update: 2017, September, 29th

Organism: human

ISOdb: a database of Iso-Seq isoforms

Last update: 2018, March, 5th

Organism: 8 organisms

ISOexpresso: a database of isoform expression in cancer

Last update: 2016, June, 1st

Organism: human

Kassiopeia: a database of mutually exclusive exonomes

Last update: not found

Organism: human, fruit fly, worm, Arabidopsis

LncAS2Cancer: alternative splicing in lncRNAs in cancer

Last update: 2021, February, 8th Organism: human

MeDAS: a Metazoan Developmental Alternative Splicing database

MutSpliceDB: A database of splice sites variants with RNA-seq based evidence on effects on splicing

OncoSplicing

Last update:

oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species

Last update:

Pan-cancer repository of validated natural and cryptic mRNA splicing mutations

Last update: not found

Organism: human

PID: Plant Intron Database

Last update

Plant Alternative Splicing Database

Last update: 2019

Organism: 15 plant genomes

PlantCircNet:

PlantSPEAD: a splicing-related protein expression database

Last update: 2017

Organisms: plants

PolyA_DB: a database of pre-mRNA cleavage and polyA sites

Last update: 2018, August. 107 human samples, 246 mouse samples, 11 rat samples, 9 chicken samples.

Organisms: human, mouse, rat, chicken

ProSAS: a database of the effects of alternative splicing events on the structure of the resulting protein isoforms.

Last update: not found. Published in 2008.

Organism

RJunBase: a database of RNA splice junctions in human normal and cancerous tissues

RBPDB

Last update:

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

SpliceAid: a database of experimentally proven RNA target motifs bound by splicing proteins in human

Last update: 2013, February

Organism: human

SpliceAid2: a database of human splicing factors expression data and RNA target motifs

Last update: 2013 February: 71 splicing factors, 2,339 RNA binding sites

Organism: human

SpliVap

TassDB: a tandem splice sites database

Last update: not found. Published in 2010.

TCGA SpliceSeq: splicing patterns alternation in TCGA

Last update: not found

TeaAS: a database of alternative splicing in tea plants

Last update

TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence

TSVdb: TCGA splicing variants database

Last update: 2020, May, 9th (the last commit)

VastDB: a database of alternative splicing profiles

Last release: 2020, December, 21st

VirusCircBase: a database of virus circular RNAs

Visualization

DoChaP: a domain-splicing visualization

Last release:

Jutils: A visualization toolkit for differential alternative splicing events

Benchmark studies

Splice variants

Splicing