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MAJIQ specifications


Unique identifier OMICS_15693
Alternative name Modeling Alternative Junction Inclusion Quantification
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.1
Stability Beta
Registration required Yes
Maintained Yes




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  • person_outline Yoseph Barash

Publications for Modeling Alternative Junction Inclusion Quantification

MAJIQ citations


Computational identification and validation of alternative splicing in ZSF1 rat RNA seq data, a preclinical model for type 2 diabetic nephropathy

Sci Rep
PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x

[…] isoforms. in this study, we chose salmon, one of the top performers in speed and accuracy based on our internal evaluation, for this type of analysis. tools in the second category include miso, majiq, and rmats, which can be used to analyse rna-seq data at the exon level and to detect known and novel splicing events. these latter methods are especially useful for organisms with limited […]


ICE1 promotes the link between splicing and nonsense mediated mRNA decay

PMCID: 5896957
PMID: 29528287
DOI: 10.7554/eLife.33178.037

[…] we asked whether the observed increases in uorf-containing mrnas could be attributed to alterations in splicing. we detected alternative splicing events using two independent software packages, majiq and leafcutter, and excluded any genes found to undergo of splicing changes upon ice1 depletion by either algorithm, using permissive cutoffs (; see materials and methods for details; [; ]). […]


SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program

PMCID: 5963917
PMID: 29741478
DOI: 10.7554/eLife.37419.041

[…] intron etc), but rather individual splice junctions). it might be worth considering using one of the analysis pipelines that analyses "events" and provides a deltapsi output (e.g. miso, rmats, majiq…)., 4) data supporting a role for srsf3 in regulating mrna stability or other events (figure 6). these data are either counterintuitive or are difficult to understand at the gene level. […]


Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation

PLoS Biol
PMCID: 5636171
PMID: 28961236
DOI: 10.1371/journal.pbio.2002623

[…] a deeper analysis of changes in splicing of eif2b5 was carried out to closely examine inclusion of intron 12 and to validate the occurrence of this ri using another method; the software package majiq [] was used to assess local splicing variation in eif2b5 for annotated and de novo splice events. a hypoxia-induced increase in expression of intron 12 was confirmed using this approach (), […]


Integrative deep models for alternative splicing

PMCID: 5870723
PMID: 28882000
DOI: 10.1093/bioinformatics/btx268

[…] offers a scalable integrative solution to improve splicing code modeling as vast amounts of relevant genomic data become available., availability and implementation: code and data available at:, contact: [email protected] , supplementary information: are available at bioinformatics online., a key contributor to transcriptome complexity is alternative […]


Quantitative analysis of cryptic splicing associated with TDP 43 depletion

BMC Med Genomics
PMCID: 5446763
PMID: 28549443
DOI: 10.1186/s12920-017-0274-1

[…] with >30m reads per sample), we instead suggest using one of the several recently released tools that can identify and classify unannotated splice junctions such as junctionseq [], leafcutter [], majiq [] or sgseq []., the inherent flexibility of our pipeline results in a large number of false positive hits which have to be aggressively filtered downstream. the initial cryptic exon discovery […]

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MAJIQ institution(s)
Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, USA
MAJIQ funding source(s)
Supported by R01 AG046544.

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