Search Results for "linkage" - Page 2
Sort By:
Showing 68 open source projects for "linkage"
View related business solutions-
Custom VMs From 1 to 96 vCPUs With 99.95% UptimeLive migration and automatic failover keep workloads online through maintenance. One free e2-micro VM every month.
-
Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
-
1
ART-DeCo
ART-DeCo uses polymorphism allelic ratio to predict contaminations
...Those are in turn used for detection of contamination with a screening test, followed by identification and quantification of the contaminant. ART-DeCo can be implemented in any NGS workflow, from gene panel to genome-wide analyses. Any polymorphism is helpfull. Rare SNPs and SNPs in linkage disequilibrium should be taken into account to consolidate predicted contaminations. -
2
CoVaMa
Co-Variation Mapper
...CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome. These tables are then analysed for evidence linkage disequilibrium. CoVaMa requires python version 2.7 and Numpy. -
3
Piplin
Open source self-hosted continuous integration and deployment system
...Support multi-environment deployment of the project (you can create multiple environments such as development, testing, pre-release and production by yourself). Support linkage deployment, for example: after the development environment is successfully deployed, the test environment can be automatically triggered to start the deployment. -
4
wgssat_nbfgr
WGSSAT: SSR Annotation Pipeline
...The mining of SSRs from whole genome provides valuable information on the abundance of SSRs in various genomic regions and will also facilitate the development of markers for genetic analysis and related applications, such as marker-assisted breeding and linkage mapping. -
Cut Data Warehouse Costs by 54%BigQuery delivers 54% lower TCO with exabyte scale and flexible pricing. Free migration tools handle the SQL translation automatically.
-
5
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.
-
6
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.... -
7
Lep-MAP2
Linkage map construction suite
Note: Lep-MAP3 is now available https://sourceforge.net/projects/lep-map3/. Expect 20x-1000x speedup over LM2 and more accurate maps. Lep-MAP2 is a novel linkage map construction software suite. Please refer to the wiki for its documentation. For further information, please contact Pasi Rastas, pasi.rastas@gmail.com. If you use Lep-MAP2, please cite Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example P. Rastas, F.C.F. Calboli, B. ... -
8
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. ... -
9
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... -
Veeam Data Platform v13.1Try Veeam Data Platform today. Experience the unified platform that's secure by design, portable by default, and proven to recover clean, fast, and anywhere.
-
10
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).
-
11
debug_mutex
c/c++ debug-mutex library
A cross-platform implementation of a mutex, that automatically checks for everything, you might be doing wrong: - DeadLocks - Invalid mutex leave order - Thread Shutdown, while still holding mutex locks - Destroying a locked mutex - (Un)Locking a destroyed mutex - UnLocking an unlocked mutex - UnLocking an mutex locked by another thread - Locking a non-recursive, locked mutex - Not destroying all mutexes before application termination Every abnormal produces a console... -
12
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 -
13
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.
-
14
SimpleMap
A tool to streamline high density genetic linkage group constrcution
-
15
Kmeans and Average linkage clustering methods. The Readme is included with the jar file, but the file itself is executable. All that is required is that the data files be set up such that each line is another set of data points with each dimension being separated by a space. For further understanding look at data1.txt - data4.txt. The Readme explains how to run the file
-
16
Lep-MAP
fast and accurate linkage map construction for large SNP datasets
Lep-MAP is a novel linkage map construction software. Note there is a new version, Lep-MAP2 available in https://sourceforge.net/projects/lepmap2/ Also note a bug in Lep-MAP: genotype alleles should be given in numerical order like "1 2", not as "2 1". If you use Lep-MAP, please cite Lep-MAP: fast and accurate linkage map construction for large SNP datasets Pasi Rastas; Lars Paulin; Ilkka Hanski; Rainer Lehtonen; Petri Auvinen Bioinformatics 2013; doi: 10.1093/bioinformatics/btt563 -
17
GwasLD
Quick search the LD SNPs against reported GWAS Catalog.
we invented a simple desktop stand-alone program (GWAS-LD) and also web-based program to identify the previous GWAS SNPs and the reported traits in high linkage disequilibrium (LD) state with a query SNP. To make the program, we downloaded all GWAS SNPs from GWAS catalogue database (http://www.genome.gov) and investigated all proxy (in 1 Mbp) SNPs which was in high LD (r2 = 0.9) with the reported GWAS SNPs by SNAP program (http://www.broadinstitute.org/mpg/snap). -
18
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. -
19
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 -
20
OACoder
OACoder: Postcode coding tool
...The Output Area Classification (OAC) is a free geodemographic classification. It is an Office of National Statistics validated measure that summarises neighbourhood conditions at the Output Area Level across the United Kingdom. Linkage of this valuable statistics has been problematic for users more used to address records that are georeferenced using unit postcodes. OACoder resolves this problem by allowing users to link corresponding OAC codes to each of the postcode addresses. This software is made available under a GPL-3.0 license, and is described in the following paper: Muhammad Adnan, Alex Singleton, Paul A. ... -
21
rnasimulase
Simulation of allele-specific RNA-seq data
Simulation of allele-specific RNA-seq data -
22
HIVCD
Informatics tool for contamination screening in the HIV sequencing lab
HIVCD is an informatics tool developed to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. Full details can be found in our paper titled "Application of a new informatics tool for contamination screening in the HIV sequencing laboratory" The code provided is a simple user interface to the underlying algorithm. We provide it as a convenience but it comes with absolutely no warranty as stated in the Apache License, Version 2.0. -
23
POConfItemBuddy
Extension for Project Open's Conf Items
POConfItemBuddy extends Project Open's Conf Items to include features like logical server groupings, software relationships to servers, and application relationships to application containers (like Tomcat or ESB). -
24
Webtracks
Building a federated science web one link at a time
Webtracks’ objective is to develop an approach and mechanism for constructing and propagating structured information to describe the linkage between distributed research objects in the context of academic activities. -
25
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.