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LDlink
Allows users to query pairwise linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs). LDlink is a web-based LD analysis tool providing access to several bioinformatics modules. The software integrates expanded population reference sets, updated functional annotations, and interactive output to explore possible functional variants in high LD. It can facilitate mapping of disease susceptibility regions and assist researchers in characterizing functional variants based on genotype-phenotype associations with potential clinical utility.
LDAK / Linkage-Disequilibrium Adjusted Kinships
A software for computing LD-adjusted kinships. The original use of LDAK was to adjust for linkage disequilibrium (LD) by calculating SNP weightings which downweight the contribution of SNPs in highly tagged regions. LDAK now also includes MultiBLUP, a method for creating linear prediction models. This improves upon standard BLUP by allowing for multiple kinship matrices. Either the user can provide these kinship matrices, or they can be determined using Adaptive MultiBLUP.
LDheatmap
Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria (LD) between single nucleotide polymorphisms (SNPs). From a data set that provides information on pairwise LD between SNPs in a genomic region, it plots color-coded values of the pairwise LD measurements and returns an object containing several components. The package also contains two functions which can be used to highlight or mark with a symbol pairwise LD measures on an LD heat map.
AVENGEME / Additive Variance Explained and Number of Genetic Effects Method of Estimation
Provides joint estimation of chip heritability and the proportion of variants affecting the trait based on polygenic scores. AVENGEME can be applied when only summary data is available for individual markers and this allows to be readily applied to the increasingly large datasets that are now being made available by study consortia. AVENGEME is able to estimate the genetic model parameters underlying large-scale association studies.
LOCO-LD / LOcalization COrrection using LD
Uses a probabilistic model to describe the allele frequencies and the linkage patterns within short genomic windows. LOCO-LD is an approach to performing spatial localization corrected for linkage-disequilibrium (LD). This package is designed primarily to work in a supervised manner by using training data from individuals whose origins are known. It performs well when only a fraction of the genome is given, suggesting that it is appropriate for the analysis of genomic fragments extracted from admixed individuals.
LDstore
Enables sharing of linkage disequilibrium (LD) information needed for accurate fine-mapping in the era of biobank-scale datasets. LDstore serves for estimation, storage, and seamless sharing of LD information. It uses parallel computing and sparse storage of LD information to achieve small file sizes. This method is useful to collect LD information for the trait-associated genomic regions enabling accurate fine-mapping from summary statistics and thus allow multiple causal variants without time-consuming communication and repeated analysis efforts across the participating cohorts.
STOPGAP / Systematic Target OPportunity assessment by Genetic Association Predictions
Contains genetic associations and genes that influence human traits. STOPGAP is a genetic association and functional genomics data to supply more evaluation of the gene scores and variant-to-gene ranking hypotheses. This tool supports target validation. It uses functional annotation dataset and several key algorithms for (1) combining the genome wide association study (GWAS) dataset, (2) calculating linkage disequilibrium (LD), (3) evaluating the gene scores and variant-to-gene ranking hypotheses in order to generate a set of STOPGAP datasets. This tool is available in desktop or web application.
GLIDERS / Genome-wide LInkage DisEquilibrium Repository and Search engine
Allows users to investigate local and long-range associations between all HapMap phase 2 and 3 single nucleotide polymorphisms (SNPs). GLIDERS is a web-based application for interrogating linkage disequilibrium (LD). It provides a quick list of potential proxy SNPs and an indication of the extent of LD between the potential proxies and the query SNP(s). It also provides insight into potential SNP mapping errors or more interesting biological processes by revealing strong associations between SNPs on different chromosomes.
Linkage Disequilibrium with Several Options
Serves for the QTL detection. LDSO uses fine-mapping methods or studies about genome-wide association to produce this QTL detection. This tool helps for studying the population histories. This study focuses on simulations of whole diploid population histories under various historical scenarios based on the gene-dropping method. Output files can explain several statistics about the population chosen by the user (inbreeding rates, allele frequencies, linkage disequilibrium (LD)).
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