A list of alternative splicing analysis resources
Last release: 2021, February, 3rd
Last release: 2011, October, 29th
Last release: not found
Last release: 2016, January, 29th
Last release: 2019, May, 7th
Last release: 2021, February, 22nd
Last release: 2020, July, 24th
- URL
- PubMed
- GitHub
- [Pubmed HISAT-3N] (https://pubmed.ncbi.nlm.nih.gov/34103331/)
Last release: 2019, February, 8th
Last release: 2021, March
Last release: 2019, May, 30th (the last commit)
Last release: 2019, May, 5th
Last release: 2013, July, 2013
Last release:
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
Last release: 2018, December, 25th
Last release: 2011, August, 10th
Last release: 2018, August, 6th (the last commit)
Last release: 2010, October, 23rd
Last release: 2020, May, 13th
featureCounts is a part of Subread to count features expression
Last release: 2021, February, 20th
Last release: 2013, November, 25th
Kallisto-Splice is a part of a tool for a splice-aware mapping
Last release: 2021, January, 14th
Last release: 2014
The R code is in the supplementary materials
Last release: 2018, April, 17th
Last release: 2020, June, 22nd
Last release: 2017, February, 25th
Last release:
Last release: 2020, November, 13th
Last release: 2018, April, 3rd
Last release: 2018, November, 28th
Last release: not found
Last release: 2018, July, 4th (the last commit)
Last release: 2019, February, 26th
Last release: 2020, September, 5th (the last commit)
Last release: 2019, December, 3rd
Last release: 2012, May, 14th
Last release: not found
Last release: 2021, January, 28th (the last commit)
Last release: not found
Last release: not found
Last release: 2015
Last release: not found
Last release: 2021, February, 16th
Last release: 2020, August, 27th
Last release:
Last release: 2017, July, 4th. Not maintained.
Last release: 2019, July, 2019
Last release: 2019, January, 30th (the last commit)
KISSDE for differential splicing analysis Last release: 2020, July, 2nd
Last release: not found
Last release: 2016, December, 8th (the last commit)
Last release: 2015, August, 4th
Last release: not found
Last release: 2021, February, 16th
Last release: 2019, September, 4th
Last release: 2021, February, 8th
Last release: 2017, May, 24th
Last release: not found
Last release: 2018, December, 12th (the last commit)
Last release:not found
Last release: 2019, November, 19th
Last release: not found
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
The tool detects events, compares between samples and predicts the consequence on a protein structure
Last release: 2014, February, 21st
Last release: 2019, October, 24th (the last commit)
Last release: 2015, July, 31st
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34017946/)
- [Github] (https://github.com/CraigIDent/SpliSER)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34152934/)
- [Github] (https://github.com/ablifedev/SUVA)
Last release: 2017, February, 7th
Last release:
Last release: 2021, March
Last release: 2019, November, 27th
Last release:
Last release: 2020, November, 23rd (the last commit)
Last release: not found. Not maintained.
Last release: not found
Last release: 2020, December, 11th
Last release: not found
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34480063/)
- [GitHub] (https://github.com/henryxushi/BayesDenovo)
Last release: 2017, March, 19th
Last release: 2019, August, 12th (the last commit cjBitSeq)
Laste release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34589189/)
- [URL] (http://cosbi4.ee.ncku.edu.tw/DEIso/)
Last release: 2017
Last release: 2012, November, 17th
Last release: 2019, February, 12th
Last release: 2017, May, 17th
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34674629/)
- [URL] (http://bioinfolab.unl.edu/emlab/consemble/ )
- 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
Last release: 2013, January, 1st
Last release: 2017, December, 20th (the last commit of BayesDRIMSeq)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34469510/)
- [Github 1] (https://github.com/TobiTekath/DTUrtle)
- [GitHub 2] (https://tobitekath.github.io/DTUrtle/)
Last release:_ not found_
Last release: 2019, April, 9th
Last release: 2014, April, 1st
Last release: not found
Last release:
Last release: not found
Last release: 2020, May, 11th
Last release: 2020, December, 3rd
Last release: not found
Last release: 2017, April, 3rd
Last release: not found
Last release: 2010, September, 9th
Last release: 2015, May, 5th (the last commit)
Last release: 2012, November, 17th
Last release: 2017, September, 14th
Last release: 2014, October, 15th
Last release:_ not found_. Published in 2014.
sleuth is a differential isoform expression tool after kallisto analysis
Last release: 2020, February, 13th
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34698224/)
- [GitHub] (https://github.com/BiodataAnalysisGroup/metaDIEA)
Last release: 2019, November, 11th
Last release: 2019, May, 17th. No longer maintained.
Last release: 2016, March, 18th
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34686194/)
- [GitHub] (https://github.com/Oshlack/MINTIE)
Last release: 2013, April, 18th
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34033544/)
- [GitHub] (https://github.com/jzbio/MultiTrans)
Last release: not found
Last release: 2016, June, 27th (the last commit)
Last release: not found. Published in 2013.
Last release: 2011, December, 6th
Last release: 2020, June, 9th
Last release: 2020, December, 28th
Last release: 2020, December, 20th
Last release: not found
Last release: 2013, October, 25th
Last release: 2013, October, 14th
Last release: 2021, February
Last release: 2020, June, 19th (the last commit)
The variant of the tools is pRSEM: an isoform quantification from a complementary data Last release: 2020, February, 14th
Last release: not found. Published in 2013
Last release:
Last release: 2016, April, 14th
Last release: 2020, November, 26th
Last release: 2017, March, 15th (the last commit)
Last release:
Last release:_ not found_. Published in 2014.
Last release: 2012, May, 17th
Last release: 2017, August, 23rd
Last release: 2017, October, 11th
Last release: 2014, April, 24th
Last release:_ not found_. Published in 2014
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34499147/)
- [Bioconductor] https://www.bioconductor.org/packages/release/bioc/html/SplicingFactory.html
Last release: 2021, March, 4th
Last release: 2018, February, 22nd
Last release: 2021, January, 8th
Last release: 2015, February, 19th
Last release: 2018, February, 19th
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34254977/)
- [Sourceforge] (https://sourceforge.net/projects/transassembly/files/)
Last release: 2014, September, 2nd
Last release: 2020, September, 9th (the last commit)
Last release: 2015, January, 24th
Last release: 2018, December, 29th (the last commit)
Last release: 2018, July, 5th
ChopStitch: an exon identification and splice graph construction out of transcriptome assembly and WGS
Last release: 2018, November, 8th
Part of the sysSeq package.
Last release: 2015, July, 17th (the last commit)
Last release: not found. Published in 2020.
Last release: 2017, September, 5th
Last release: 2021, February, 10th
Last release: 2010, November, 25th
The tool can quantify exon expression
Last release: 2020, April, 18th
Last release: 2016, April, 13th
Last release: not found
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/33906938/)
- [GitHub] (https://github.com/evendrow/Intron-Essentiality/)
Last release: not found
Last release: not found
Last release: 2017, September, 26th
The tool also detects differentially regulated exons. MISO also presents sashimi plots for exon expression visualisation.
Last release: 2019, May, 17th. No longer maintained.
Last release: 2018, March, 19th
Last release: 2016, January, 6th
Last release: 2015, June, 29th (the last commit)
Last release: 2021, February, 15th
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34266387/)
- [GitHub] (https://github.com/vrmelo/SPLICE-q)
Last release: 2013, May, 17th
Last release: 2019, September, 27th (the last commit)
Last release: 2020, November, 3rd
Last release: 2018, June, 22th
Last release:
- [URL] (https://fivex.sph.umich.edu)
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34459872/)
- [Github] (https://github.com/statgen/fivex)
Last release: 2013, March, 12th
Last release:
Last release: 2015, June, 29th
Last release: 2013, October, 15th
Last release: not found
Laste release: 2008
Last release:
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Last release: 2015, May
Last release: 2010
Last release:_ not found_
Last release: not found
Last release:_ not found_
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34349788/)
- [URL] (https://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice2)
Laste release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/31138913/)
- [URL] (https://kipoi.org/)
Last release:_ not found_
Last release: 2018, July, 3rd
Last release: 2021, February, 20th
Last release:
Laste release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/33893808/)
- [URL] (https://www.genecascade.org/MutationTaster2021/)
Last release:_ not found_
Last release: 2017, May, 30th
Last release: _ not found_
Last release: 1997, January
Last release: 2019, May, 15th
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)
Last release: 2019, May, 18th
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/30804562/)
- [URL] (http://bejerano.stanford.edu/scap/)
- [Bitbucket] (https://bitbucket.org/bejerano/splicing_classifier/)
Last release: 2013, July, 12th
Last release: 2011, March, 2nd
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/25525159/)
- [URL] (http://www.openbioinformatics.org/annovar/spidex_download_form.php)
Last release: 2019, August, 7th
Last release: 2020, March, 7th
Last release:
Last release: not found
Laste release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34088258/)
Last release:
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34289339/)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/28794409/)
- [URL] (http://trap-score.org/)
Last release: 2017, May, 22nd (the last commit)
Last release: not found
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34668517/)
- [URL] http://bioserv.mps.ohio-state.edu/dsRBPBind
Last release: 2019 August 7th
Last release: not found
Last release: not found
Last release: 2013, January, 13th (the last commit)
Last release: 2019, February, 20th
Last release: 2021, February
Last release: 2020, March, 20th
Last release: 2020
Last release: 2016
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34410342/)
- [Github] (https://github.com/yushanqiu/WDFSMF)
jcast: takes in alternative splicing events and returns custom protein sequence databases for isoform analysis
Last release: March, 2021 (the last commit)
QUILTS: the identification of novel proteins, resulting from single nucleotide variants, splice variants and fusion genes
Last release: not found
Last release: 2019, April, 29th
Last release: 2017, June 21st (the last commit)
Last release: 2018, May, 28th
TopPG: a proteogenomic tool for generating proteoform sequence databases with genetic alterations and alternative splicing events
Last release: 2017, October, 18th (the last commit)
Last release: not found
Last release: December, 2018
Last release: 2019, April, 3rd
Last release: not found
Last release: 2018, June, 3rd
- PubMed BRIE
- [Pubmed BRIE2] (https://pubmed.ncbi.nlm.nih.gov/34452629/)
- GitHub
- [Pypi] (https://pypi.org/project/brie/)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34469510/)
- [Github 1] (https://github.com/TobiTekath/DTUrtle)
- [GitHub 2] (https://tobitekath.github.io/DTUrtle/)
Last release:
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34353340/)
- [GitHub] (https://github.com/salzmanlab/SICILIAN)
Last release: 2016, July, 7th (the last commit)
Last release: not found
Last release: 2020, August, 20th
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:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34253685/)
- [GitHub] (https://github.com/marabouboy/FLAME)
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34140043/)
- [Github] (https://github.com/WGLab/LIQA)
Last release: 2020, May, 22nd
Last release: 2017, March, 23rd
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34302453/)
- [GitHub] (https://github.com/ksahlin/ultra)
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/30535380/)
- [GitHub] (https://github.com/dls03/DeepIsoFun/)
Last release: 2020, October, 29th
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34282449/)
- [URL] (http://www.sdu-idea.cn/codes.php?name=DMIL-Isofun)
Last release:
Last release: 2019, April, 11th
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34046593/)
- [Bitbucket] (https://gitlab.com/bu_cnio/trifid)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34185647/)
Last release:
Last release: 2020, February, 26th
Last release
Last release
Last release:
Last release: 2019, February, 27th
Last release: 2021, March, 15th
Last release: 2020, August, 17th
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34252942/)
- [Github] (https://github.com/hallogameboy/JEDI)
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34663689/)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34556162/)
- [GitHub] (https://github.com/avigayel/SRCP)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34031440/)
- [GitHub] (https://github.com/tgen/bisbee)
ACEScan: the algorithm for prediction of conserved alternatively spliced exons from pairs of conserved mouse/human exons (Upon request)
Last release: 2005, July, 10th
ASES: a tool for assessing the impact of alternative splicing, initiation and termination of transcription on protein diversity in evolution
Last release: 2020, December, 16th
Last release: 2020, May, 24th
Last release: 2015, December, 9th (the last commit)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34563123/)
- [GitHub] (https://github.com/itmat/CAMPAREE)
Last release: 2020, June, 30th
eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34104972/)
- [URL] (https://eskip-finder.org)
Last release: 2020, February, 11th
Last release: 2015, September, 3rd
Last release: not found
Last release: 2019, May, 27th
Last release: 2021, January, 21st
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34099673/)
- [Bitbucket] (https://bitbucket.org/biociphers/moccasin/src/master/)
Includes rMATS and DEXSeq Last release: not found
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34674638/)
Last release
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34316711/)
- [URL] (https://galantelab.github.io/reboot/)
Last release: 2020, April, 23rd
Last release: 2018, March, 26th
Last release: 2016, November, 18th
Last release: 2017, October, 26th
Last release: 2019, august, 2nd
Last release: 2020, July, 6th
SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
Last release:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34266979/)
Last release: 2018, May, 24th
Last release: 2019
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
Last update: 2012, October, 16th
Organisms: human, mouse, rat, worm, arabidopsis
Last update: 2008, September, 5th
Organisms: human, mouse, rat
- PubMed
- FTP
Last update: 2021
Organisims: 19 vertebrate and invertebrate genomes
Last update
- [URL] (www.peptideatlas.org/builds/arabidopsis/)
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34411258/)
Last update
- [URL] (http://ascot.cs.jhu.edu/)
- [GitHub] (https://github.com/jpling/ascot)
Last update: 2019, June, 25th
Organisms: cattle, sheep, pig, chicken, horse
Last update: 2017, June, 30th
Organisims: human
Last update: 2017, May, 4th, 196,446 splicing events
Organism: human
Last update:
- [URL] (http://jianglab.org.cn/ASPN/)
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34285345/)
Last update: 2021
Organism: human
Last update: 2021
Organism: cucumber
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs
Last update: 2017, December, 21st
Organism: human
Last update:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34493866/)
- [URL] (https://www.ebi.ac.uk/eqtl/)
Last update:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/33497435/)
- [URL] (https://ccsm.uth.edu/ExonSkipAD/)
Last update: not found
Organism: Human
Last update: 2011, December, 26th
Organism: human
Last update: 2017, September, 29th
Organism: human
Last update: 2018, March, 5th
Organism: 8 organisms
Last update: 2016, June, 1st
Organism: human
Last update: not found
Organism: human, fruit fly, worm, Arabidopsis
Last update: 2021, February, 8th Organism: human
Last update:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34554251/)
- [URL] (http://www.oncosplicing.com/)
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species
Last update:
- [URL] (http://rnabiology.ircm.qc.ca/oRNAment/)
- [Pubmed] (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145663/)
Last update: not found
Organism: human
Last update
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34111777/)
- [URL] (http://biodb.sdau.edu.cn/PID/index.php)
Last update: 2019
Organism: 15 plant genomes
Last update: 2017
Organisms: plants
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
Last update:
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/21036867/)
- [URL] (http://rbpdb.ccbr.utoronto.ca/)
recount3: an online resource consisting of RNA-seq gene, exon, and exon-exon junction counts as well as coverage
- Pubmed
- [URL] Does not work
SpliceAid: a database of experimentally proven RNA target motifs bound by splicing proteins in human
Last update: 2013, February
Organism: human
Last update: 2013 February: 71 splicing factors, 2,339 RNA binding sites
Organism: human
- URL
- [PubMed]
Last update: not found. Published in 2010.
Last update: not found
Last update
- [URL] (http://www.teaas.cn/index.php)
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34154536/)
Last update: 2020, May, 9th (the last commit)
Last release: 2020, December, 21st
Last release:
- Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders
- Benchmarking deep learning splice prediction tools using functional splice assays
- Exon identity influences splicing induced by exonic variants and in silico prediction efficacy
- [Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers] (https://pubmed.ncbi.nlm.nih.gov/34174808/)