Search Results for "linkage"
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Showing 23 open source projects for "linkage"
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A software package that implements the probabilistic record linkage technique (PRL). This is a new, improved, open-source, multi-platform version of the previously available program, by the same authors.
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Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.
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TASSEL
TASSEL is a bioinformatics software package
TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics. -
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Pyslvs
Open Source Planar Linkage Mechanism Simulation and Synthesis Software
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Open Source Data Quality and Profiling
World's first open source data quality & data preparation project
This project is dedicated to open source data quality and data preparation solutions. Data Quality includes profiling, filtering, governance, similarity check, data enrichment alteration, real time alerting, basket analysis, bubble chart Warehouse validation, single customer view etc. defined by Strategy. This tool is developing high performance integrated data management platform which will seamlessly do Data Integration, Data Profiling, Data Quality, Data Preparation, Dummy Data... -
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NOVA
Analysis and visualization of complexome profiling data.
NOVA is a program designed to analysis complexome profiling data (Heide et al., 2012). A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. ... -
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Dynamic Linkage
Dynamic Linkage Social Aggregation Model
This project will create a user-friendly modeling system for studying animal social aggregations. The model codifies the a new hypothesis that the animal's state, kinematics, and the group's emergent properties are dynamically linked together, with each one affecting the others. The model will be constructed using Object-Oriented MatLab. -
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Slim is a data compression system for scientific data sets, a binary and a library with C linkage. Slim works with integer data from one or more channels in a file, which it can compress more effectively and more rapidly than general tools like gzip.
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SPAWNN
SPatial Analysis With self-organizing Neural Networks
The SPAWNN toolkit is an innovative toolkit for spatial analysis with self-organizing neural networks which is particularily useful for spatial analysis, visualization and geographical data mining. To run the toolkit, simply download and execute (double-click) the jar-file. Please cite: - Hagenauer, J., & Helbich, M. (2016). SPAWNN: A Toolkit for SPatial Analysis With Self-Organizing Neural Networks. Transactions in GIS, 20(5), 755-775. Other related publications: - Hagenauer, J.... -
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Gene-Environment iNteraction Simulator 2
A tool able to simulate gene-environment and gene-gene interactions.
Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. ... -
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PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
...We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities." *Please cite this paper if you use this code for your research -
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CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems. Reads GFF3 data and produces a PNG or SVG image.
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SimpleMap
A tool to streamline high density genetic linkage group constrcution
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MendelScan
Variant scoring and linkage mapping for family exome sequencing
MendelScan is a tool for prioritizing candidate variants in family-based studies of inherited disease. -
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cvsba
OpenCV wrapper for sba library
...The main features are: - Based on sba-1.6, one of the most popular and robust bundle adjustment implementation, which is extensively used and tested by the community - sba installation is not needed since it is included in cvsba - New CMake structure which makes the library compilation, installation and linkage easier - Similar interface than Bundle Adjustment implementation on cv::LevMarqSparse::bundleAdjust() - Include examples to test the library on synthetically generated data - GPL licence -
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rnasimulase
Simulation of allele-specific RNA-seq data
Simulation of allele-specific RNA-seq data -
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Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.
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Populating Research Data Australia (RDA) with collection descriptions of Australian-related biomolecular data held in the European Bioinformatics Institute (EBI) databanks. This project is ANDS-funded through the DIISR Education Infrastructure Fund.
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slclust: a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. The slclust utility is written in ANSI C++.
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Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.
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HaploPainter - a pedigree and haplotypes drawing tool written in Perl/Tk. The software processes pedigree information in standard linkage formats combining haplotype information outputs from Simwalk, Genehunter, Allegro and Merlin.
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febrl-gen is a Java-based frontend to Febrl, an open-source data linkage system written in Python. Users can configure the parameters of a linkage project through the frontend, and febrl-gen will generate a Febrl-ready configuration file.
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