Search Results for "disease" - Page 2
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Showing 139 open source projects for "disease"
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CorThiZon
Cortical Thickness of brain by Zones
CorThiZon is a Matlab toolbox. MRI 3D T1 images are treated to estimate cortical thickness by zones in native and normalized space. It uses a Laplace-based technique following brain segmentation. Results can be easily reported in Excel files for further statistical analysis. If you use this toolbox, please reference: ‘Early diagnostic of Alzheimer’s disease using cortical thickness: impact of cognitive reserve', Querbes O, Aubry F, Pariente J, Lotterie JA, Démonet JF, Duret V, Puel M... -
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The Disease Ontology has moved to Github. New project page: https://github.com/DiseaseOntology Disease Ontology is a stuctured controlled vocabulary originally based upon and mapped to medical billing codes. The goal of this ontology is to create a comprehensive hierachical controlled vocabulary to represent subsumptive disease relationships.
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MWI spinal cord atlases
Normative atlases for the spinal cord using myelin water imaging
... of abnormalities in individuals with myelin-related disease and damage. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31407400. -
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W2MHS-DNN
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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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
This repository contains the most updated code version of MANTIS, the Multi-locus ANTIgenic Simulator R-package. MANTIS is developed and maintained by the Evolutionary Ecology of Infectious Disease (EEID) research group at the Department of Zoology, University of Oxford, UK. For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN ACCESS... -
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Nuvarator
A SNV Detection Software Tools Installer Package
... available to researchers interested in evolutionary biology, and hence lays the foundation for predicting disease susceptibility and drug response. It a GUI based software having an automated, easy to use user interface designed in shell script. It is available online at https://sourceforge.net/projects/Nuvarator It is open source and also includes a user manual which aids the user in its installation. -
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PD_BiochemicalSystemsTheory
A model of Parkinson’s disease using biochemical systems theory
Major pathways involving in Parkinson's disease (PD) such as alphasynuclein aggregation, dopamine synthesis, lewy body formation, tau phosphorylation, parkin, and apoptosis were modeled using stochastic differential equations. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. The model allows a qualitative analysis of PD... -
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VacSol
An in slico pipeline to predict potential therapeutic targets
Infectious diseases are emerging rapidly throughout the globe, and antibiotic resistant bacterial strains lead to the therapeutic failure; ultimately causing the high risk of cost and re-infection. Vaccination is considered as one of the most effective mechanisms for the treatment of a particular disease; and conventional vaccinology approaches have rendered certain limitations against some pathogens. Reverse vaccinology and subtractive proteomics are novel competent computational approaches... -
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Hetionet
Hetionet: an integrative network of disease
Hetionet is a hetnet — network with multiple node and edge (relationship) types — which encodes biology. The hetnet was designed for Project Rephetio, which aims to systematically identify why drugs work and predict new therapies for drugs. The JSON and Neo4j formats contain node and edge properties, which are absent in the TSV and matrix formats, including licensing information. Therefore the recommended formats are JSON and Neo4j. Our hetio package in Python reads the JSON format, but it... -
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HPOSim
Analysis phenotypic similarity between genes and between diseases
This package implements multiple similarity measures for HPO terms, genes and diseases. It is aiming at phenotype analysis for gene sets and disease sets. Functions for HPO enrichment analysis is also provided. -
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HGPEC
A tool for gene and phenotype prioritization and evidence collection
Finding gene-disease and disease-disease associations are important issues in the biomedical area and many prioritization methods have been proposed for this goal. Among these, approaches based on heterogeneous network of genes and phenotypes were considered state-of-the-art ones, which can use for diseases with/without known molecular basis. Here, we develop a Cytoscape plugin, namely HGPEC, based on a ran-dom walk with restart algorithm on a heterogeneous network of genes and phenotypes... -
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Apkinson
Android application for Parkinson's disease monitoring
Apkinson aims to provide a mobile monitoring solution for patients suffering from Parkinson's disease. It is capable of detecting phone calls, record the speech of the patient during the call, and afterwards analyze the signal with respect to certain features to evaluate the progression of the disease. Additionally, it collects a variety of meta information to put the analysis results into a deeper context. Speech processing modules are meant to be attached via AIDL. Apkinson does not yet... -
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E2F1Map
Logic based simulations of E2F1 regulatory core for disease signatures
We provide comprehensive molecular interaction map of E2F1 transcription factor in tumor progression and metastasis. We provide various scripts, boolean based models to identify molecular signatures for predicting EMT phenotype in bladder and breast cancer model. -
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decd
R package for complex disease analysis
This is a R packages designed for complex disease when large scale expression data is available -
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CVDdb
Cerebrovascular Disease database
Our integrated database schema is an add-on schema to Loris (http://loris.ca/, Das et al, 2011), and includes 3079 subjects and over 550 federated and searchable data items including imaging details, medical history and examination, stroke and laboratory details, which maps to large multi-centre stroke trials with imaging data from over 10,000 patients from 30 countries. Here we provide our current version of our schema, and data dictionary. The data itself is for internal access only during... -
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Random Bits Regression
Random Bits Regression is a strong general predictor.
We proposed an accurate, robust and fast general predictor (RBR) for regression and classification in big data era. The application of this method is very broad, from science to industry, finance and health. The accuracy and robustness improvement of our method over existing method could bring huge benefits in some critical applications. For example, natural disaster prediction, stock price prediction, personal/population disease prediction. The fast-speed nature of our method not only allows... -
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing... -
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PExFInS
Post-GWAS Explorer for Functional Indels and SNPs
The generation of Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) was originated from the observation that high proportion of cis-acting expression quantiative trait loci (cis-eQTLs) emerged in GWAS SNPs and the underexplored status of indel cis-eQTLs for GWAS. We believe that the integration of cis-eQTLs, especially indel cis-eQTLs, with candidate disease-associated variants generated from GWAS could facilitate the identification of causal genes or disease mechanisms. On the other... -
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... be used for downstream analysis including assembly to identify genes that are differentially abundant between groups of metagenomes (e.g., healthy vs diseased). Please refer to our RECOMB paper for more details: Wontack Han, Mingjie Wang and Yuzhen Ye. A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes. Proceeding of RECOMB 2017.
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Rapid Inquiry Facility
A tool used to support environmental health studies.
The Rapid Inquiry Facility (RIF) is a freely available software application that supports two types of environmental health activities: disease mapping studies and risk analysis studies. It was designed to help epidemiologists and public health researchers to rapidly investigate potential environmental hazards, especially those related to industrial sites. The tool uses health, environmental, socioeconomic, population and geographic data to calculate risks in relation to sources of exposure... -
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MeningoAfrica
Implementation of a meningococcal disease model
Implementation of a meningococcal disease model for the African belt. -
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MetaOpen
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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Simple GWAS catalogue pruner
Prune GWAS SNPs for a trait based on distance from each other.
Select rows from GWAS catalogue dataset https://www.ebi.ac.uk/gwas/docs/downloads based on p value, and then rows matching a disease trait term e.g. 'height' and optional exclude rows not matching a disease trait term e.g. 'bmi' - helpful for precisely matching a gwas e.g. you only want height not 'height adjusted bmi'. Also it will prune the SNPs by distance, as used by haploreg. The user can select the distance. If two SNPs are within the user defined distance then the more proximal one... -
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MutAid
MutAid: Sanger and NGS based pipeline for mutation screening.
... mapping, variant calling, variant annotation and co-analyze Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as deletions and insertions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms (Sanger, Illumina, 454 and Ion Torrent) and five read mappers including BWA,TMAP, Bowtie,Bowtie2 and GSNAP and four variant...