LFE is a collection of about 70 modular scripts to explore, edit and manage large tabular text files. Some files are too lare to be manipulated with programs like MS Excel. For example in genome research (genome-wide association alaysis) it is not uncommon to have tabular files hudreds of millions rows long. LFE was designed to handle these large files. LFG outputs graphics based on large files.
ALLELE is a toolkit for performing various analyses and conversions for genome research. Not fully posted yet.
Manhattan Harvester can automatically detect mathematically "promising" peaks from Manhattan Plot data by setting various filters. It also does statistics for the peaks it encounters.
RegScan is a fast method to perform genome wide association studies (GWAS). It specializes on analyzing combinatorial phenotypes (for example phenotype ratios) and is able to simultaneously analyze any number of phenotypes. Published in 2015.
A script to assign quantitative ancestry components to individuals based on similarity matrices that are computed using reference populations. Published in 2017.
Fizard is a graphical user interface (GUI) tool for studying images of fluorescent objects. It can quantify objects from the images in an interactive manner as well as automatic manner. More broadly, Fizard can be used to analyze any photo.
In genome-wide association studies (GWAS) it is often important that the dataset does not contain closely related individuals. This script is used for cleaning genotype datasets of closely related individuals in such a way that the remaining dataset retains the maximal number of individuals possible. RelOut allows to set the degree of genetic distance as a threshold value for cleaning the file. This can be combined with call rate info or phenotype info to ensure that the remaining data are of maximal quality. The input for this script is produced by PLINK. ATTN! RelOut is out-dated; the newest version of Relout is available as part of ALLELE (see above).
Fuzzy is an implementation of FP-Grow algorithm in order to study associations within datasets - namely the associations rules. The program was written with biological applications in mind. So far it has been mainly used to study associations between phenotypic features.
PopSel is a tool for case - control studies in biological research (GWAS). After the cases have been selected (for example the patients with a certain disease) typically a control group from among the healthy individuals needs to be compiled. It may be important that the controls resemble the caseses as closely as possible with the disease being the only main difference. PopSel is able to perform pairwise matching between the cases and the potential controls as well as ensure that the distributions of the selected features are the same within both groups. For example the gender, age, and body weight are distributed in a similar manner. ATTN! PopSel is out-dated; the newest version of PopSel is available as part of ALLELE (see above).
FamTree is an ongoing project. The aim is to use a novel graphical method to determine how well an individual belongs to a certain group in terms of genetic distance. This program can be used to clean data for GWAS studies.
This software package is for studying MALDI-MS spectra of pectin fragments. Both the positive and nengative mode are supported. Several functions for spectral annotation are available.
CMR is a tool to model drug release from eroding nanoparticles. It is used to predict drug delivery from nanoparticles in blood.
Reference: A voxel-based Monte Carlo model of drug release from bulk eroding nanoparticles, J Nanosci Nanotechnol. 2010 Sep;10(9):5903-7.