Search Results for "disease" - Page 4
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Showing 139 open source projects for "disease"
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OVPDT
A family-based association test for sequencing data
OVPDT is a family-based association test designed for analyzing sequencing data. It considers the effects of both common and rare variants on a complex disease. It also takes the directions of effects for causal variants into account. -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation and several recessive disease genes have been discovered with the help of this technique in consanguineous families. The researchers typically use SNP arrays to determine... -
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pvaas
Program to identify Variants Associated with Aberrant Splicing
Alternative splicing is a precisely regulated process that involves interactions between cis- and trans-acting regulatory elements, and factors that disrupt these interactions can result in aberrant splicing. About 15-60% of human disease-causing mutations affect mRNA splicing rather than directly affecting coding sequences (López-Bigas, et al 2005, Krawczak M, et al, 1992). Deep transcriptome sequencing (RNA-seq) provides ability to interrogate both aberrant splicings and mutations... -
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VarImpact
Extracting effects of mutations on molecular properties from text.
Genetic variants alter cellular behavior in a variety of ways, changing biochemical properties of DNA, mRNA, and proteins. Many large-scale sequencing projects are under way to detect human variation in health and disease. Although broad disease associations can be discovered by GWAS studies, the low-level impact of mutations is hardly available in structured form. The results of thousands of small-scale experiments, on the other hand, are present in the literature and discuss observations made... -
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LoDel
A probabilistic model for detecting low-frequent somatic deletion
LoDel is a Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. LoDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples. The important features of LoDel are: •Estimation of accurate mutation frequency in a mixed disease sample •Improved somatic deletion calling based on the probabilistic model with the parameter... -
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PathNER
A tool for systematic identification of biological pathway mentions
... between disease and pathways. The latest updates will be on GitHub : https://github.com/chengkun-wu/PathNER -
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WM Hyperintensities Segmentation Toolbox
Open Source White Matter Hyperintensities Segmentation Toolbox
Wisconsin White Matter Hyperintensity Segmentation [W2MHS] and Quantification Toolbox is an open source MatLab toolbox designed for detecting and quantifying White Matter Hyperintensities (WMH) in Alzheimer’s and aging related neurological disorders. WMHs arise as bright regions on T2- weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer’s disease (AD) with regard to its prognosis. Our toolbox... -
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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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Snp Viewer
A program for visualising Affymetrix SNP array data
A program for visualising Affymetrix SNP array data for identification regions of homozygosity. Written to aid autozygosity mapping and aid the discovery of potential disease loci. -
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NAADSM
A framework for simulating the spread and control of animal diseases
NAADSM is a framework for creating stochastic, spatial, state-transition simulation models of the spread and control of highly contagious diseases of animals. User-established parameters define model behavior in terms of disease progression; disease spread by animal-to-animal contact, contact with contaminated personnel or equipment, and airborne dissemination; and the implementation of control measures such as vaccination and depopulation. Resources available to implement disease control... -
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RODS (Real-time Outbreak and Disease Surveillance) is a real-time computer-based public health surveillance system initially developed at the RODS Laboratory, University of Pittsburgh for the early detection of disease outbreaks .
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Boundary Shift Integral
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PathMEN
A Java tool for mining pathway mentions from literature
... between disease and pathways. -
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Vector-borne diseases such as dengue inflict a terrible burden on humankind. There is a desperate need for low-cost solutions to operationally improve prevention and control. Cell phones are appropriate because dengue is an urban disease.
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Test
Healthcare
... for Disease Control and Prevention (CDC) in collaboration with the Department of Health and Human Services (HHS), Assistant Secretary for Public Affairs office (ASPA), and the Food and Drug Administration’s (FDA) Center for Tobacco Products (CTP). https://syndication.hhs.gov/ http://tools.cdc.gov/ http://tools.niaid.nih.gov/ http://tools.fda.gov/ -
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
... interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. Contact: bmhoan@gmail.com or walter.vincent.fr@gmail.com -
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NIOSH_BViewer
NIOSH Digital Radiograph Viewer for B Readers
... Division of Respiratory Disease Studies National Institute for Occupational Safety and Health Morgantown, WV The BViewer software was designed and implemented by Thomas L. Atwood, Ph.D. Southeast X-Ray, Inc. (479)667-4000 -
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RVASSOC is a simple program for performing various tests for association between genotypes and disease status using sequence variants from unrelated cases and controls. It was designed to accommodate both rare variants and missing genotypes.
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MetCore
Metabolomics Bioinformatics Tools
...-mass spectrometry (LC-MS), and comprehensive two-dimensional gas chromatography-mass spectrometry (GCxGC/TOF-MS). Each type of analysis affords limited analyte coverage of molecules present in a patient sample and therefore provides only a partial molecular profile for an individual patient. These diverse analytical data must be integrated with advanced bioinformatics methods for accurate evaluation of health and detection of disease susceptibility. -
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Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.
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SPA - SNP based pathway analysis
SNP based pathway analysis
Name: SPA Full name: SNP based pathway analysis Maintainer: jiangyongshuai@gmail.com liuguiyou1981@163.com Language: R package Description: SPA is an R package which can identify disease or phenotype related pathways. Input rs# and GWAS test p-values, you can get the related pathways. -
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The Matlab files described here refers the simulation described in the paper : “Rule-Based Model of Chronic Disease Epidemiology: Elderly Depression as an Illustration”, under submission in Plos One. Installation and user guide including example is inserted in the global .zip file (Appendix 5.pdf)
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Global Epidemic Simulator
A platform for modelling influenza-like epidemics and containment
The Global Epidemic Simulator is a platform for modelling directly transmissible human diseases such as influenza, and testing intervention policies that may reduce the duration or severity of an outbreak of such a disease. Building on previous work, this model is spatial and individual-based, using various geographical and demographic data sources to place households at absolute locations, populated with individuals of specific ages who each attend schools or workplaces situated... -
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Breast Cancer Diagnosis System
System diagnosing breast cancer in mammograms
... with malignant invasive breast tissue by a series of image processing steps. Primary prevention seems impossible since the causes of this disease are still unknown. -
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Colony
An ant simulation game involving user interaction.
Colony is an opensource two-dimensional game developed in Python and Pygame as an educational learning experience by Jonathan Redeker. Ants spawn and live in their colony breeding, feeding, and hoping they will not die of disease. The user plays as a god destroying their colony with different skills depicted by their "player points". Colony is compiled with PyInstaller and the music and sound effects were created by lunarfox (http://www.facebook.com/lunarfox, http://soundcloud.com/lunarfox)