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|Alternative name||Isoform Usage Two-step Analysis|
|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
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Publication for Isoform Usage Two-step Analysis
Transcriptome Profiling of Huanglongbing (HLB) Tolerant and Susceptible Citrus Plants Reveals the Role of Basal Resistance in HLB Tolerance
[…] 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
[…] 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
[…] 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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