Microarray probe tools [Python]

This set comprises of various utilities used to analyze microarray probe sequences and to convert probe data between various formats.

MicroarrayHPC [Python]

This is a set of applications designed to test various hypothesis on extremely large number of samples from various microarray experiments

MirMod [Bash/R]

MirMod algorithm was designed to cope with miRNA NGS data, especially to detect miRNAs 3' end modification. Moreover, it indicates origin of each detected sequence in samples, thus obtained results could be used for further analysis.

miRNA tools [Python]

This is a set of applications used to gather and analyse nucleotide sequence data, based mainly on the UCSC and NCBI databases. For a complete list of applications please check the detailed description.

Sequence feature tools [Python]

This is a set of applications used to gather and analyse nucleotide sequence data, based mainly on the UCSC and NCBI databases. For a complete list of applications please check the detailed description.

Sequencing tools [Perl/R]

Sequencing tools package includes the following applications: Sequence counter [Perl] - Memory efficient package used for counting sequences in a set of fastq files, Seed sequencing [R] - Program for miRNA sequencing data seed summarization (Seed sequencing), Family members generator [R] - Program for indication of interfering miRNA isoforms.

GMM Spectra [Matlab]

GMM_spectra is an application for modeling mass spectra with the use of Gaussian mixture model to obtain significant features of the signal. It is a fully automatic method which has a potential to adapt to signal of various complexity.

modEM_GPU [Matlab]

Scripts provide parallel realization of modified expectation-maximization algorithm for estimating Gaussian mixture model parameters in 1D spectra modeling. Model is currently used in analysis of mass spectrometry data and nuclear magnetic resonance spectra.

ADFIT [Matlab]

ADFIT is a set of scripts in MATLAB environment to parameter estimation for mathematical models described by system of ordinary dierential equations

HKG stability [R]

This is a set of scripts that can be used to assess stability of genes in experiments with treating factors

miRPCR [R]

miRPCR can be used to standardize RT-qPCR results obtained for various miRNAs using snRNA/snoRNA as a reference, test for statistical significance between various conditions and to visualize the results.