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eQTL software tools and databases

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…
GTEx
Dataset

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…

Blood eQTL…
Web

Blood eQTL browser

Provides all trans-eQTLs detected at a somewhat less stringent false discovery…

Provides all trans-eQTLs detected at a somewhat less stringent false discovery rate (FDR) of 0.5, to enable more in-depth post-hoc analyses. Blood eQTL browser is a web app available for all…

G T A T C G C T A
SCAN
Web

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…

WASP
Desktop

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…

Braineac
Dataset

Braineac Brain eQTL Almanac

Presents a large, exon-specific expression quantitative trait loci (eQTL) data…

Presents a large, exon-specific expression quantitative trait loci (eQTL) data set covering ten human brain regions. Braineac offers to the scientific community a valid instrument to investigate the…

GOAL
Desktop

GOAL

Detects single-nucleotide polymorphisms (SNPs) that regulates expression of…

Detects single-nucleotide polymorphisms (SNPs) that regulates expression of genes. GOAL is based on a Bayesian approach which infers cis regulatory polymorphisms underlying gene expression…

TreeQTL
Desktop

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…

GMAC
Desktop

GMAC Genomic Mediation analysis with Adaptive Confounding adjustment

Performs genomic mediation analysis with adaptive confounding adjustment. GMAC…

Performs genomic mediation analysis with adaptive confounding adjustment. GMAC is tailored for but not limited to genomic mediation analysis, restricting to scenarios with the presence of…

Mash
Desktop

Mash Multivariate Adaptive Shrinkage

Allows to analyse genomic datasets that measure many effects in many…

Allows to analyse genomic datasets that measure many effects in many conditions. Mash facilitates more quantitative assessments of effect-size heterogeneity than simple…

SPIRE
Desktop

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…

KG-SCCA
Desktop

KG-SCCA Knowledge-Guided Sparse Canonical Correlation Analysis

Aims for improving learning results by incorporating valuable prior knowledge.…

Aims for improving learning results by incorporating valuable prior knowledge. KG-SCCA is a knowledge-guided sparse canonical correlation analysis (SCCA) algorithm able to model two types of prior…

QRank
Desktop

QRank Quantile Rank-score based test

Provides an easy way to identify eQTLs that are associated with the conditional…

Provides an easy way to identify eQTLs that are associated with the conditional quantile functions of gene expression. QRank is a Quantile Rank-score based test which complements the existing…

FastQTL
Desktop

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…

PEER
Desktop

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…

asSeq
Desktop

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…

QGene
Desktop

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…

eQtlBma
Desktop

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…

G T A T C G C T A
eQTLseq
Desktop

eQTLseq

Implements two classes of statistical models for detecting simultaneously…

Implements two classes of statistical models for detecting simultaneously multiple associations between gene expression and genomic polymorphisms in a population. eQTLseq uses paired DNA-seq and…

xQTL Serve
Desktop

xQTL Serve

Performs quantitative trait locus (xQTL) analyses on a multi-omic dataset that…

Performs quantitative trait locus (xQTL) analyses on a multi-omic dataset that consists of RNA sequence (RNA-seq), DNA methylation, and histone acetylation (H3K9Ac ChIP-seq) data. xQTL Serve is a…

CONFETI
Desktop

CONFETI Confounding Factor Estimation Through Independent component analysis

Identifies broad impact expression quantitative trait loci (eQTL). CONFETI is…

Identifies broad impact expression quantitative trait loci (eQTL). CONFETI is an analysis framework which provides a method for finding broad impact eQTL while leveraging the advantages of…

EnsembleExpr
Desktop

EnsembleExpr

Predicts massively parallel reporter assays (MPRA) reporter expression level…

Predicts massively parallel reporter assays (MPRA) reporter expression level from sequence, and predicts which sequence variants will lead to significant allele-specific expression. EnsembleExpr is a…

AraQTL
Dataset

AraQTL

Aims to support the Arabidopsis and plant genetics community to utilities eQTL…

Aims to support the Arabidopsis and plant genetics community to utilities eQTL (expression quantitative trait loci) data in their research. AraQTL stores and combines all published Arabidopsis eQTL…

iSet
Desktop

iSet

Enables testing for interactions between context and sets of variants, and…

Enables testing for interactions between context and sets of variants, and accounts for polygenic effects. iSet is a module that provides control for population structure, either using principal…

iBMQ
Desktop

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…

Lasso
Desktop

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…

geQTL
Desktop

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…

eQTL databases
Dataset

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…

Sherlock
Web

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…

MT-eQTL
Desktop

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…

GEPdb
Dataset

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…

GDL
Desktop

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…

HEFT
Desktop

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…

Group-Wise-EQTL
Desktop

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:…

GenAMap
Desktop

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…

eqtl.uchicago.e…
Web

eqtl.uchicago.edu

Represents novel functional sites with DNA-level variation relevant to many…

Represents novel functional sites with DNA-level variation relevant to many human phenotypes and health. The eqtl.uchicago.edu is a web browser to both summarize the results of these studies and to…

seeQTL
Dataset

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,…

Matrix eQTL
Desktop

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…

xQTL workbench
Web

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…

EPSILON
Desktop

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…

FastMap
Desktop

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…

Reveal
Desktop

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…

LORS
Desktop
Meta-eQTL
Desktop

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…

kruX
Desktop

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…

ICE
Desktop

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…

QTL store
Dataset

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…

RTeQTL
Dataset

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…

eQTL Viewer
Web

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…

eQTL Browser
Web

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…

eLMM
Desktop

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.

Genevar
Web

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…

PANAMA
Desktop

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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