OPROGRAMOWANIE


MrGSEA



MATLAB implementation of Gene Set Enrichment Analysis (GSEA) method for finding pathways which can show more complex relation between changes of gene expression due to different phenotypes. Major adjustments of the method:
- 12 gene ranking metrics implemented (plus its ranks and/or absolute values)
- possibility to use external ranking metric method (by applying own function)
- possibility to use external Gene Set Database
- phenotype permutation available for all ranking methods (even external ranking)
- increased efficiency by parallel computing used

Autor: Michał Marczyk

Pliki:
Download



BatchI



R package with the batch effect identification by dynamic programming algorithm implementation.

Autor: Anna Papież

Pliki:
Package source
Windows binaries



GaMRed



GaMRed is a fully automatic application for filtering insignificant features, which can process different kinds of high-throughput data e.g. microarray, qRT-PCR or RNA-Seq. The method is based on adaptive algorithms for estimation of the cut-off threshold using Gaussian mixture model and k-means clustering. The proposed software supports both Windows and Mac OSX operating systems.
Authors: Marczyk M, Jaksik R, Polanski A, Polanska J

Autor: Michał Marczyk

Pliki:
Software download
Manual