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Non-coding variant effect prediction software tools | Whole-genome sequencing data analysis

G T A T C G C T A
CADD
Desktop
Web

CADD Combined Annotation Dependent Depletion

Scores the deleteriousness of single nucleotide variants as well as…

Scores the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. CADD integrates many diverse annotations into a quantitative score. The basis of…

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LINSIGHT
Desktop

LINSIGHT

Provides a generalized linear model for functional genomic data and genome…

Provides a generalized linear model for functional genomic data and genome annotations. LINSIGHT is a computational method that outperforms state-of-the-art prediction methods in the task of…

deltaSVM
Desktop

deltaSVM

A sequence-based computational method to predict the effect of regulatory…

A sequence-based computational method to predict the effect of regulatory variation, using a classifier (gkm-SVM) that encodes cell type-specific regulatory sequence vocabularies. The induced change…

G T A T C G C T A
DeepSEA
Web
Desktop

DeepSEA

A deep learning-based algorithmic framework for predicting the chromatin…

A deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity. DeepSEA can accurately predict the epigenetic state of a…

G T A T C G C T A
FATHMM-XF
Web
Desktop

FATHMM-XF

Allows prediction of the functional consequences of non-coding and coding…

Allows prediction of the functional consequences of non-coding and coding single nucleotide variants (SNVs). FATHMM-XF is a method consisting in an improvement over the predictor FATHMM-MKL. The…

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GWAVA
Desktop
Web

GWAVA Genome Wide Annotation of VAriants

Supports prioritization of noncoding variants by integrating various genomic…

Supports prioritization of noncoding variants by integrating various genomic and epigenomic annotations. The GWAVA web server allows users to retrieve precomputed scores from each of the three…

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cepip
Desktop

cepip

Provides context-dependent epigenomic weighting for regulatory variant…

Provides context-dependent epigenomic weighting for regulatory variant prioritization. Cepip is a context-dependent model that could examine important chromatin features surrounding an eQTL and…

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PRVCS
Desktop

PRVCS Predicting regulatory variant with composite statistic

An integrative resource for predictions from eight different tools on…

An integrative resource for predictions from eight different tools on functional annotation of noncoding variants. PRVCS is designed to predict and prioritize the regulatory variants by integrating…

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FunSeq
Desktop
Web

FunSeq

This tool is specialized to prioritize somatic variants from cancer whole…

This tool is specialized to prioritize somatic variants from cancer whole genome sequencing. FunSeq contains two components: 1) building data context from various resources; 2) variants…

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INFERNO
Web
Desktop

INFERNO INFERring the molecular mechanisms of NOncoding genetic variants

Provides a method to determine functional genetic variants underlying genetic…

Provides a method to determine functional genetic variants underlying genetic association signals and to characterize their tissue-specific effects on regulatory elements, target genes, and…

Haystack
Desktop

Haystack

Allows characterization of hotspots of epigenetic variability across different…

Allows characterization of hotspots of epigenetic variability across different cell-types. Haystack can be applied to epigenetic mark and supplies a method to study cell-type identity and the…

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FIRE
Dataset

FIRE Functional Inference of Regulators of Expression

Scores all single nucleotide variations (SNVs) in the human genome. FIRE is a…

Scores all single nucleotide variations (SNVs) in the human genome. FIRE is a genome-wide variant annotation tool that predicts the potential of SNVs to regulate gene expression, assigning higher…

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DANN
Desktop

DANN Deleterious Annotation of genetic variants using Neural Networks

Annotating genetic variants, especially noncoding variants, for the purpose of…

Annotating genetic variants, especially noncoding variants, for the purpose of identifying pathogenic variants remains a challenge. CADD is an algorithm designed to annotate both coding and noncoding…

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GenoCanyon
Web

GenoCanyon

A whole-genome annotation method that performs unsupervised statistical…

A whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the…

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