MAJIQ statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MAJIQ

Tool usage distribution map

This map represents all the scientific publications referring to MAJIQ per scientific context
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Associated diseases


Popular tool citations

chevron_left Known transcript quantification Novel transcript quantification Alternative splicing events identification Differential usage Alternative splicing visualization chevron_right
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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

[…] cript 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 annot […]


ICE1 promotes the link between splicing and nonsense mediated mRNA decay

PMCID: 5896957
PMID: 29528287
DOI: 10.7554/eLife.33178.037
call_split See protocol

[…] the authors (). Reads mapping to constitutive exons and introns of Ensembl GRCh37.87 annotations were quantified with HTSeq (), and a read cutoff stringency of 0.99 was used for REMBRANDTS analysis. Majiq and Leafcutter were used to analyze splicing changes following siICE1 and siNT treatment (; ). For Majiq, a change in isoform usage of 10% or greater at the 95% confidence level was used to iden […]


Integrative deep models for alternative splicing

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

[…] truct their models, we use it to compare the old and new models. We generated genomic features and PSI quantification for ∼12 000 cassette exons used in () for this dataset for the five tissues using MAJIQ () and AVISPA (). The second dataset, denoted MGP Data, was prepared by () and it contains RNA-Seq data from six tissues (heart, hippocampus, liver, lung, spleen and thymus) with average read co […]


DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates

PMCID: 5870796
PMID: 28595376
DOI: 10.1093/bioinformatics/btx357

[…] in stage 1 is fed to the conjugate normal-gamma model in stage 2. Some other models do take the strategy of utilizing the shared information from multiple biological replicates, such as rMATS (), and MAJIQ (). However, they are both exon-centric, quantifying and identifying alternative splicing at the exon level not the isoform level.Here, we present DEIsoM, a hierarchical Bayesian model for quant […]


Quantitative analysis of cryptic splicing associated with TDP 43 depletion

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

[…] ced 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 pip […]


A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior

Cell Rep
PMCID: 5199341
PMID: 28009295
DOI: 10.1016/j.celrep.2016.12.002
call_split See protocol

[…] samples on an Illumina Hiseq 2000 machine (three biological replicates of wild-type and Slm2 knockout CA1–CA3 regions. RNA-seq data were mapped using STAR (), and splicing changes were analyzed using MAJIQ (). […]

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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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