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MISO specifications


Unique identifier OMICS_01337
Alternative names Mixture of Isoforms, misopy, fastmiso
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An annotation file and a RNA-Seq reads
Input format GFF+SAM
Operating system Unix/Linux
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
numpy, scipy, pysammatplotlib, samtools, bedtools
Maintained Yes




No version available



  • person_outline Chris Burge
  • person_outline Edoardo Airoldi
  • person_outline Yarden Katz

Additional information


Publication for Mixture of Isoforms

MISO 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

[…] transcript 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 […]


Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing

Genome Med
PMCID: 5902843
PMID: 29665865
DOI: 10.1186/s13073-018-0538-1

[…] Unique reads from RNA-seq data in bam format are used as input for MISO (The Mixture of Isoforms), which detected AS events based on Bayes factors, filtering criteria, Psi values (Ψ) and confidence intervals []. Sashimi plots were generated to illustrate all five typ […]


Loss of TDP43 inhibits progression of triple negative breast cancer in coordination with SRSF3

Proc Natl Acad Sci U S A
PMCID: 5899436
PMID: 29581274
DOI: 10.1073/pnas.1714573115

[…] rlying the pro-oncogenic role of TDP43 in TNBC, RNA-sequencing (RNA-seq) was performed to identify the differential AS events upon TDP43 knockdown by shRNAs in the TNBC cell line MDA-MB231. Using the MISO package, we found that 1,103 splicing events demonstrated significantly changed PSI values (Bayes factor >6 and |ΔPSI| >0.2) after knockdown of TDP43 (). Gene ontology (GO) analysis revealed that […]


ZFR coordinates crosstalk between RNA decay and transcription in innate immunity

Nat Commun
PMCID: 5861047
PMID: 29559679
DOI: 10.1038/s41467-018-03326-5

[…] reference genome hg19 using STAR aligner. Differential gene expression analysis was performed using the DESeq2 package, and alternative splicing analysis was performed on pooled STAR alignments using MISO, with hg19 version 2 annotations. Events were expression-filtered to require at least one read from each isoform and at least 10 total reads, and significance was determined using the previously […]


CRISPR/Cas9 mediated ASXL1 mutations in U937 cells disrupt myeloid differentiation

PMCID: 5843401
PMID: 29532865
DOI: 10.3892/ijo.2018.4290
call_split See protocol

[…] /software.broadinstitute.org/gsea/index.jsp from the Broad Institute (Cambridge, MA, USA). Enriched gene sets were defined according to the following criteria: P<0.05 and FDR-corrected P-value <0.05. miso () was used to detect RNA splicing differences, specifically differentially regulated exons or isoforms.For RT-qPCR, total RNA was reverse transcribed to cDNA using the SuperScript III First-Stra […]


Identifying Host Molecular Features Strongly Linked With Responses to Huanglongbing Disease in Citrus Leaves

Front Plant Sci
PMCID: 5836289
PMID: 29541089
DOI: 10.3389/fpls.2018.00277

[…] en the four datasets were observed in response to HLB. The quantitative visualization of splice junction of the genes showing significant psi score difference was done using “sashimi_plot” program in MISO (Mixture of Isoforms) tool along with uninfected sample as sashimi plot (Supplementary Figures and Supplementary Table ). The sashimi plot shows the number of reads corresponding to specific exo […]


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MISO institution(s)
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Department of Statistics and FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA
MISO funding source(s)
Supported by grants from the US National Science Foundation and the US National Institutes of Health.

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