MiMSeg



The package contains algorithm for automated detection of tumor tissue on NMR apparent diffusion coefficient maps. The algorithm itself may be sued for segmentation of any lesions on basically any medical image, however adjustments are required. In case of any problems please contact: Ten adres pocztowy jest chroniony przed spamowaniem. Aby go zobaczyć, konieczne jest włączenie w przeglądarce obsługi JavaScript..
After sucessful usage please cite:

Binczyk Franciszek, Bram Stjelties, Christian Weber, Michael Goetz, Klaus Maier-Hein, Hans-Peter Meinzer, Barbara Bobek-Billewicz, Rafal Tarnawski, Joanna Polanska: MiMSeg - an algorithm for automated detection of tumor tissue on NMR apparent diffusion coefficient maps. Information Sciences, 2017, 384:235-248, doi:10.1016/j.ins.2016.07.052

Autor: F. Binczyk, J.Polanska



Spec-GMM



Matlab implementation of the efficient algorithm for Gaussian mixture modeling of spectra of different types (e.g., MALDI-ToF profiling, MALDI-IMS, NMR spectroscopy). The main idea is automated partitioning of spectral signal into fragments. The obtained fragments are separately decomposed into Gaussian mixture models. The parameters of the mixture models of fragments are then aggregated to form the mixture model of the whole spectrum.

Autor: Polanski, Marczyk, Polanska

Pliki:
Download Spec-GMM



2DGMMgel



A three step algorithm for analysis of 2D gel electrophoresis images. The main idea is based on improving the efficiency of spot detection performed with any algorithm, by fitting mixture of 2D normal distributions. The algorithm is implemented in MATLAB R2016b.

Autor: Michał Marczyk

Pliki:
Download 2DGMMgel
Annotated datasets



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
Package vignette



Divisive ik-means algorithm for MALDI IMS



Matlab library for automated segmentation of MALDI IMS data

Autor: Joanna Polanska

Pliki:
divisive_ik-means_for_MALDI_IMS



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