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
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: 2019, August, 7th
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: 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
Last release: 2017, February, 7th
Last release:
Last release: 2021, March
Last release: 2019, November, 27th
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: 2017, March, 19th
Last release: 2019, August, 12th (the last commit cjBitSeq)
Last release: 2017
Last release: 2012, November, 17th
Last release: 2019, February, 12th
Last release: 2017, May, 17th
- 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:_ not found_
Last release: 2019, April, 9th
Last release: 2014, April, 1st
Last release: not found
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: 2019, November, 11th
Last release: 2019, May, 17th. No longer maintained.
Last release: 2016, March, 18th
Last release: 2013, April, 18th
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: 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: 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
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: 2013, May, 17th
Last release: 2019, September, 27th (the last commit)
Last release: 2020, November, 3rd
Last release: 2018, June, 22th
Last release: 2013, March, 12th
Last release:
Last release: 2015, June, 29th
Last release: 2013, October, 15th
Last release: not found
Last release: not found
Laste release: 2008
Last release:
Last release: 2015, May
Last release: 2010
Last release:_ not found_
Last release: not found
Last release:_ not found_
Last release:_ not found_
Last release: 2018, July, 3rd
Last release: 2021, February, 20th
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: 2013, July, 12th
Last release: 2011, March, 2nd
Last release: 2020, March, 7th
Last release:
Last release: not found
Last release:
Last release: 2017, May, 22nd (the last commit)
Last release: not found
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
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
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
Last release:
Last release: 2016, July, 7th (the last commit)
Last release: not found
Last release: 2020, August, 20th
Last release: 2020, May, 4th
Last release: 2020, May, 22nd
Last release: 2017, March, 23rd
Last release: 2020, October, 29th
Last release: 2020, February, 26th
Last release: 2019, February, 27th
Last release: 2021, March, 15th
Last release: 2020, August, 17th
ACEScan: the algorithm for prediction of conserved alternatively spliced exons from pairs of conserved mouse/human exons (Upon request)
Last release: 2005, July, 10th
Last release: 2020, December, 16th
Last release: 2020, May, 24th
Last release: 2015, December, 9th (the last commit)
Last release: 2020, June, 30th
Last release: 2020, February, 11th
Last release: 2015, September, 3rd
Last release: not found
Last release: 2019, May, 27th
Last release: 2021, January, 21st
Last release: 2019, April, 11th
Includes rMATS and DEXSeq
Last release: not found
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
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: 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: 2021
Organism: human
Last update: 2021
Organism: cucumber
Last update: 2017, December, 21st
Organism: human
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: not found
Organism: human
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
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
Last update: not found. Published in 2010.
Last update: not found
Last update: 2020, May, 9th (the last commit)
Last release: 2020, December, 21st