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IUTA specifications


Unique identifier OMICS_05872
Alternative name Isoform Usage Two-step Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained No


No version available

Publication for Isoform Usage Two-step Analysis

IUTA citations


Transcriptome Profiling of Huanglongbing (HLB) Tolerant and Susceptible Citrus Plants Reveals the Role of Basal Resistance in HLB Tolerance

Front Plant Sci
PMCID: 4923198
PMID: 27446161
DOI: 10.3389/fpls.2016.00933

[…] ive exons (MXE) and retained intron (RI) events, from replicate RNA-Seq data. We also detected the differential isoform usage of each genes between HLB tolerant and HLB susceptible citrus trees using IUTA (Niu et al., ). […]


Genetic Characterization of ExPEC Like Virulence Plasmids among a Subset of NMEC

PLoS One
PMCID: 4723317
PMID: 26800268
DOI: 10.1371/journal.pone.0147757

[…] pathotype, all plasmids to be sequenced had to contain at least two plasmid-borne virulence genes from a list of nine commonly associated with large ExPEC virulence plasmids (ompTp, hlyF, cvaC, etsA, iutA, iroN, tsh, iss, sitC). Imposition of this selection criterion ensured that only plasmids containing some virulence associated genes would be included, and that cryptic or other plasmids were exc […]


Evaluation of methods for differential expression analysis on multi group RNA seq count data

BMC Bioinformatics
PMCID: 4634584
PMID: 26538400
DOI: 10.1186/s12859-015-0794-7

[…] esolution in current DE analysis: gene-, transcript-, exon-, and base-level. Examples of the DE methods for individual levels are (i) edgeR [], DESeq [], and TCC [] for gene-level; (ii) Cuffdiff2 [], IUTA [], and SplicingCompass [] for transcript-level; (iii) DEXSeq [] and NPEBseq [] for exon-level; and (iv) DER Finder [] for base-level. Many methods can perform DE analysis for multiple levels (e. […]


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IUTA institution(s)
Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA

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