:: DESCRIPTION
degPrune is a program for pruning most non-differentially expressed genes from microarray data in PCL or NCBI GEO format
::DEVELOPER
Machine Learning and Evolution Laboratory (MLEG)
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
BMC Genomics. 2010 Nov 2;11 Suppl 2:S3. doi: 10.1186/1471-2164-11-S2-S3.
Density based pruning for identification of differentially expressed genes from microarray data.
Hu J1, Xu J.
:: DESCRIPTION
SpectralTDF is a program for computing the transition density function (TDF) of the diffusion approximation of the Wright-Fisher process with general diploid selection and recurrent mutation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes.
Steinrücken M, Jewett EM, Song YS.
Bioinformatics. 2015 Nov 9. pii: btv627.
:: DESCRIPTION
Twilight is a standalone script for analysis, visualization, and annotation of a pre-filtered set of protein/ligand complexes deposited with the PDB with ligand RSCC values that are below a threshold of 0.6.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):195-200. doi: 10.1107/S1744309112044387.
Visualizing ligand molecules in Twilight electron density.
Weichenberger CX1, Pozharski E, Rupp B.
:: DESCRIPTION
DEEGEP is a simple statistical method for testing for natural selection from a high dimensional (i.e. multiple population) allele frequency spectrum. The method uses a neutral control defined by the user (e.g. intergenic sites) to learn a background neutral distribution. This is accomplished by approximating the density with a finite expansion of Gegenbauer polynomials, inspired by Kimura’s classic result in theoretical population genetics. One can then test for natural selection on a second set of putatively functional sites (e.g. microRNAs) by comparing the multi-population allele frequency spectrum to the neutral control.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
