RNAseqR

RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries. It is a C++ coded program currently compiled for Linux systems.

With GUI and command line interfaces, it can do log, PPM, and/or RPKM (if lengths provided) transformations, as well as, statistical analysis for differential expression, using the negative binomial cumulative distribution function (CDF) or the R test statistic introduced for EST analysis by Stekel, et al.

Output allows for decisions based on CDF probabilities, top R values, or comparison of R values with randomized data. Comparisons are the believability metric of Stekel et al, or observed vs expected R at a given mean expression. Randomization is through Poisson or negative binomial distributions, or column shuffling.

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License

GNU General Public License version 3.0 (GPLv3)

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Additional Project Details

Operating Systems

Linux

Programming Language

C++

Related Categories

C++ Bio-Informatics Software

Registered

2011-11-18

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