Expression quantitative trait loci (eQTLs) are genetic variants that affect gene expression. In eQTL studies, one important task is to find eGenes or genes whose expressions are associated with at least one eQTL. The standard statistical method to determine whether a gene is an…
Genotype-Tissue… Genotype-Tissue Expression

GTEx Genotype-Tissue Expression

Correlations between genotype and tissue-specific gene expression levels will…

Correlations between genotype and tissue-specific gene expression levels will help identify regions of the genome that influence whether and how much a gene is expressed. GTEx will help researchers…

Web app
G T A T C G C T A SNP and CNV Annotation SNP and CNV Annotation

SCAN SNP and CNV Annotation

A large-scale database of genetics and genomics data associated to a…

A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories…

Desktop app
Multivariate Adaptive… Multivariate Adaptive Shrinkage

Mashr Multivariate Adaptive Shrinkage

Analyzes genomic datasets that measure many effects in many conditions (e.g.…

Analyzes genomic datasets that measure many effects in many conditions (e.g. gene expression changes under many treatments). Mashr increases power, improves effect-size estimates, and facilitates…

Desktop app
Software for… Software for Polymorphism Identification…

SPIRE Software for Polymorphism Identification Regulating Expression

A pipeline for expression Quantitative Trait Loci (eQTL) processing. SPIRE…

A pipeline for expression Quantitative Trait Loci (eQTL) processing. SPIRE integrates different univariate and multivariate approaches for eQTL analysis, paying particular attention to the…

Desktop app
QGene QGene

QGene

Allows execution and comparison of a variety of modern QTL-mapping methods and…

Allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. QGene accommodates line-cross mating designs consisting of any arbitrary…

Desktop app
TreeQTL TreeQTL

TreeQTL

Implements a hierarchical multiple testing procedure. In the context of eQTL…

Implements a hierarchical multiple testing procedure. In the context of eQTL studies, TreeQTL provides methods allowing control of the false discovery rate or family wise error rate for the discovery…

Desktop app
multi-tissue eQTL… multi-tissue eQTL analysis

MT-eQTL multi-tissue eQTL analysis

A hierarchical Bayesian model for multi-tissue expression Quantitative Trait…

A hierarchical Bayesian model for multi-tissue expression Quantitative Trait Locus (eQTL) analysis. MT-eQTL explicitly captures patterns of variation in the presence or absence of eQTL, as well as…

Desktop app
Least absolute… Least absolute shrinkage and selection operator

Lasso Least absolute shrinkage and selection operator

A quantitative trait loci (QTL) mapping method guided by prior knowledge for…

A quantitative trait loci (QTL) mapping method guided by prior knowledge for identifying candidate genes. Lasso includes three steps: i) identifying QTLs from QTL mapping; ii) generating and…

Desktop app
WASP WASP

WASP

A suite of tools for unbiased allele-specific read mapping and discovery of…

A suite of tools for unbiased allele-specific read mapping and discovery of molecular quantitative trait loci (QTLs). WASP uses a simple approach to overcome mapping bias that can be readily…

Desktop app
geQTL geQTL

geQTL

A sparse regression method that can detect both group-wise and individual…

A sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits. geQTL can also correct the effects of potential confounders. Our method…

Desktop app
FastQTL FastQTL

FastQTL

Implements a popular cis-QTL mapping strategy in a user- and cluster-friendly…

Implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of…

GEPdb GEPdb

GEPdb

Integrates both genome-wide association studies and expression quantitative…

Integrates both genome-wide association studies and expression quantitative trait loci information, the two primary sources of genome-wide mapping for genotype-phenotype and genotype-expression…

QTL store QTL store

QTL store

An interactive interface to browse the Arabidopsis thaliana QTL database…

An interactive interface to browse the Arabidopsis thaliana QTL database 'qtl_ath'. This database provides complete QTL information (position, effect, interaction, etc.) from the analysis…

Desktop app
Group-Wise-EQTL Group-Wise-EQTL

Group-Wise-EQTL

A fast and robust approach to identify novel associations between sets of SNPs…

A fast and robust approach to identify novel associations between sets of SNPs and sets of genes. This model is a multi-layer linear-Gaussian model and uses two different types of hidden variables:…

Desktop app
Meta-eQTL Meta-eQTL

Meta-eQTL

A tool for fast eQTL meta-analysis of arbitrary sample size and arbitrary…

A tool for fast eQTL meta-analysis of arbitrary sample size and arbitrary number of datasets. Further, this tool accommodates versatile modeling, eg. non-parametric model and mixed effect models. In…

seeQTL seeQTL

seeQTL

A comprehensive and versatile eQTL database, including various eQTL studies and…

A comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser,…

Web app
eQTL Browser eQTL Browser

eQTL Browser

An expression quantitative trait locus (eQTL) represents a marker (locus) in…

An expression quantitative trait locus (eQTL) represents a marker (locus) in the genome in which variation between individuals is associated with a quantitative gene expression trait, often measured…

eQTL databases eQTL databases

eQTL databases

A cross-platform catalogue of expression quantitative trait loci derived from…

A cross-platform catalogue of expression quantitative trait loci derived from lymphoblastoid cell lines. This website provides genome-wide significant cis and trans association analysis results…

Real-Time engine for… Real-Time engine for expression Quantitative…

RTeQTL Real-Time engine for expression Quantitative Trait Loci analyses

Provides eQTL association results that are not available in existing eQTL…

Provides eQTL association results that are not available in existing eQTL databases browsers. These functions include (i) single SNP (single-nucleotide polymorphism) and (ii) two-SNP conditional eQTL…

Desktop app
Eliminate Confouding… Eliminate Confouding in eQTL studies with Linear…

eLMM Eliminate Confouding in eQTL studies with Linear Mixed Models

A program for performing eQTL analysis in the presence of two confounders: (1)…

A program for performing eQTL analysis in the presence of two confounders: (1) population structure, (2) expression heterogeneity.

Desktop app
eQtlBma eQtlBma

eQtlBma

Implements Bayesian statistical methods to detect eQTLs jointly in multiple…

Implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity…

Desktop app
Matrix eQTL Matrix eQTL

Matrix eQTL

A software tool for computationally efficient eQTL analysis. Matrix eQTL…

A software tool for computationally efficient eQTL analysis. Matrix eQTL supports additive linear and ANOVA models with covariates, including models with correlated and heteroskedastic errors. The…

Web app
xQTL workbench xQTL workbench

xQTL workbench

A scalable web platform for the mapping of quantitative trait loci (QTLs) at…

A scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype…

Desktop app
EPSILON EPSILON

EPSILON

An extendable framework for eQTL prioritization, which mitigates the effect of…

An extendable framework for eQTL prioritization, which mitigates the effect of highly connected genes and unreliable interactions by constructing a local network before a network-based similarity…

Web app
eQTL Viewer eQTL Viewer

eQTL Viewer

A web-based tool to visualize the relationships between the expression trait…

A web-based tool to visualize the relationships between the expression trait genes and the candidate genes in the eQTL regions using Scalable Vector Graphics. The plot generated by eQTL Viewer has…

Desktop app
FastMap FastMap

FastMap

A method for fast and efficient eQTL mapping in homozygous inbred populations…

A method for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature and structure of the measured single nucleotide…

Web app
GENe Expression… GENe Expression VARiation

Genevar GENe Expression VARiation

A platform of database and web services designed for data integration, analysis…

A platform of database and web services designed for data integration, analysis and visualization of SNP-gene associations in eQTL (expression quantitative trait loci) studies. With its interactive…

Desktop app
Graph-regularized… Graph-regularized Dual Lasso

GDL Graph-regularized Dual Lasso

A robust approach for eQTL mapping. GDL integrates the correlation structures…

A robust approach for eQTL mapping. GDL integrates the correlation structures among genetic markers and traits simultaneously. It also takes into account the incompleteness of the networks and is…

Desktop app
iBMQ iBMQ

iBMQ

A powerful and computationally optimized package that implements a joint…

A powerful and computationally optimized package that implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently to detect eQTLs. Model parameters are estimated…

Desktop app
Reveal Reveal

Reveal

A graph-based visualization of associations between SNPs and gene expression…

A graph-based visualization of associations between SNPs and gene expression and a detailed genotype view relating summarized patient cohort genotypes with data from individual patients and…

Desktop app
Hidden Expression… Hidden Expression Factor analysis

HEFT Hidden Expression Factor analysis

A combined multivariate regression and factor analysis method that identifies…

A combined multivariate regression and factor analysis method that identifies individual and pleiotropic effects of eQTL in the presence of unmeasured covariates/hidden factors. HEFT is a likelihood…

Desktop app
Inter-sample… Inter-sample Correlation Emended

ICE Inter-sample Correlation Emended

A statistical test for correcting for expression heterogeneity inherent in…

A statistical test for correcting for expression heterogeneity inherent in expression dataset due to confounding from unmodeled factors. ICE directly incorporates inter-sample correlation structure…

Desktop app
kruX kruX

kruX

An algorithm implemented in Matlab, Python and R that uses matrix…

An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at…

Desktop app
LOw-Rank… LOw-Rank representation to account for…
Desktop app
PEER PEER

PEER

A collection of Bayesian approaches to infer hidden determinants and their…

A collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have detected batch effects and…

Web app
Sherlock Sherlock

Sherlock

A computational algorithm to search for gene-disease associations from GWASs,…

A computational algorithm to search for gene-disease associations from GWASs, taking advantage of independent eQTL data. Sherlock is applicable to any complex phenotype. It is readily generalizable…

Desktop app
asSeq asSeq

asSeq

Establishes a statistical framework for future developments of eQTL mapping…

Establishes a statistical framework for future developments of eQTL mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or…

Desktop app
GenAMap GenAMap

GenAMap

An interactive analytics software platform that 1) automates the execution of…

An interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression…

Desktop app
Probabilistic… Deprecated Probabilistic ANAlysis of genoMic dAta

PANAMA Probabilistic ANAlysis of genoMic dAta

A probabilistic model to account for confounding factors within an eQTL…

A probabilistic model to account for confounding factors within an eQTL analysis. In contrast to previous methods, PANAMA learns hidden factors jointly with the effect of prominent genetic…

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