Search Results for "genetics"
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Showing 69 open source projects for "genetics"
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Amazon Genomics CLI
Tool to simplify the processes of deploying the AWS infrastructure
... infrastructure, providing you with an easy-to-use command-line interface to quickly setup and run genomics workflows on Amazon Web Services (AWS) specified by languages like WDL. By removing the heavy lifting from setting up and running genomics workflows in the cloud, software developers and researchers can automatically provision, configure and scale cloud resources to enable faster and more cost-effective population-level genetics studies, drug discovery cycles, and more. -
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The MIQAS project (Minimal Information for QTL and Association Studies) provides a standard for reporting of QTL and association studies in genetics (similar to the MIAME standard for microarray data).
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
... Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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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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stiletto
Stiletto: A computational model of the cerebral perforating arteries
Our project aims to develop a computational model of the cerebral perforating arteries, the structure, hemodynamics and vascular flow reactivity, autoregulation and their relation with the neurovascular unit (NVU) in health and disease. The project will provide a framework to simulate scenarios to try to better understand complex phenomena such as aging, the exposome and genetics involved in brain homeostasis and dysfunction. The stiletto project is brought by GNU Solidario. -
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est-sfs
Estimate the unfolded site frequency spectrum and ancestral states
.... For details of the method, see Keightley and Jackson, Genetics 209: 897-906 (2018). -
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Genome Information Entropy Spectrum
A code that computes information entropy spectrum of any genome.
We request users of this software to please kindly cite this article: Melvin M. Vopson, Samuel C. Robson, A new method to study genome mutations using the information entropy, Physica A: Statistical Mechanics and its Applications, Volume 584, 126383 (2021) https://doi.org/10.1016/j.physa.2021.126383 The GENIES program is a stand alone code, with an easy to use graphical interface that performs the following tasks: a) it loads up two genome files (original and mutated); b) it computes the... -
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coatli
Second and third moments of the "Site frequency spectrum".
In population genetics, the "site frequency spectrum" is an important summary statistic of the variation in aligned DNA sequences. This package contains implemented algorithms for the analytical calculation of the expected second and third moments of this spectrum (under the standard neutral Wright-Fisher model). Furthermore there are utilities to estimate these quantities from coalescent simulation (using output of the program 'ms', written by R.R. Hudson). As an add-on some small utilities... -
TeleRay transfers patient studies faster and more securely than any other method.
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Jack LIRE (Linked Record)
Quantum universal object system with referencing and genetics
Jack LIRE (Linked Record) is a quantum database-backed life-long text record diary with referencing (linking) between records, and a data library for life-long keeping of files such as documents, photographs, music and more. The diary records are fully searchable. Files can be mentioned in diary records to preserve memories, document knowledge and ideas, and more. Massive numbers of diary records and files can be permanently kept. A database located on one computer can be accessed from... -
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SVPhylA
SVPhylA: Sequence Vectorization for Phylogenetic Analyses
...-Kernel (non-lineal). In addition, genetic distances derived can be either combined between them or with the alignment-free distances. So far, SVPhylA contain a module to compare tree topologies by using different distance measures as a validation procedure. The statistical validation (bootstrap and jacknife) of the alignment-free trees is being developed SVPhylA is mostly designed to interact to MEGA (MOLECULAR EVOLUTIONARY GENETICS ANALYSIS). -
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BCAW Tool
Bio Codon Analysis Workflow Tool
BCAWT was developed using python 3.7 with build in and third-party modules. The usage of BCAWT is made to be very easy where users have only to input a fasta format file containing genes to be analyzed, and a bunch of analysis will be performed with 23 different output files -
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Boon Rules
Study the computational basis of human learning and inference
The main problem of the machine learning is to find a scientific regularity in experimental observations. Many methods may be served - from baseless guesses to an accurate investigation of models - to create a possible scientific interpretation. This approach consider on searching for underlying laws. Laws can be evoked from the massive data sets (genetics, robot sensors, social networks, adverisement) available now (so called the Big Data). -
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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by... -
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LiveGMS is a PHP/MySQL driven gene editor for the game Creatures 3 / Docking Station. It provides a platform independent online editor with most features other binary genetics editors have.
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GDxBase is a a web based resource focused on the genetics and genomics of complex diseases. Our mission is to provide a curated and integrated set of datasets and tools, across multiple diseases and model organisms, to support and promote research in this area.
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EggLib
Evolutionary Genetics and Genomics Library
EggLib has moved to http://mycor.nancy.inra.fr/egglib/ since version 3.0.0. -
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Application to estimate haplotypes and other genetics data, based on maximum likehood approach. It can handle present-absent as well as multiallelic loci.
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Forward Simulation
A Wright-Fisher forward population genetics simulation.
The forward simulation code is a tool to model evolution of a population under the Wright-Fisher model. The code incorporates population expansion, bottleneck, speciation and migration. Several selection and fitness mechanisms are available: selective sweeps, foreground selection in one region with a distinct background selection in neighboring regions, epistasis, and truncation selection. The code is implemented in the C++ programming language. -
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Extensions for the R statistical analysis system providing data types and functions for the storage, annotation, visualization, and statistical analysis of genetic data.
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SMARTPOP
Fast forward-in-time simulation software for population genetics
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SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments.
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CCH
A genetics tool that identifies genomic regions of shared ancestry
Combinatorial Conflicting Homozygosity (CCH) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry. The associated publication regarding CCH may be accessed here: http://www.biomedcentral.com/1471-2164/16/163 If...
