Supporting software and material for: "mirnaTA: a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using Normal Quantile Transformation (NQT)".
Dataset type: Software
Data released on October 06, 2014
Anderson JJ; Bishop-Lilly KA; Cer RZ; Herrera-Galeano JE; Mokashi VP (2014): Supporting software and material for: "mirnaTA: a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using Normal Quantile Transformation (NQT)". GigaScience Database. http://dx.doi.org/10.5524/100107
The microRNA Temporal Analyzer (mirnaTA) is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies. It is implemented in Perl and R package (>= 2.13.0) and can be run across multiple platforms such as Linux, Mac and Windows. The mirnaTA requires that users provide data from a minimum of two time point series and analyze up to 20 time points. To normalize data and remove technical variability, Normal Quantile Transformation (NQT) was used, and the normalized data is analyzed using linear regression model to locate any miRNAs which are differentially expressed in a linear manner. Any miRNAs with P-value<0.05 are considered statistically significant. The remaining miRNAs which did not fit in linear model are further analyzed in two different methods: (1) if the number of time points <=3, cumulative density function (CDF) of the normal distribution, and (2) if the number of time points is > 3, an analysis of variances (ANOVA) is utilized.
Here the software and scripts are all archived together in a TAR file taken from SourceForge at time of publication, it represents a snapshot in time of the package.
For the most recent up to date version please visit the mirnaTA SourceForge page.
Read the peer-reviewed publication(s):
Cer, R. Z., Herrera-Galeano, J. E., Anderson, J. J., Bishop-Lilly, K. A., & Mokashi, V. P. (2014). miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation. GigaScience, 3(1). doi:10.1186/2047-217x-3-20