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Interpretation software tools | Genomic array data analysis

Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and…
PennCNV
Desktop

PennCNV

A free software tool for copy number variation (CNV) detection from SNP…

A free software tool for copy number variation (CNV) detection from SNP genotyping arrays. PennCNV can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation…

GeneAnnot
Dataset

GeneAnnot

Explores the relationship between probe sets and genes. GeneAnnot compares the…

Explores the relationship between probe sets and genes. GeneAnnot compares the individual probe sequences with publicly available complementary DNA (cDNA) and predicted genes from GenBank, RefSeq and…

VegaMC
Desktop

VegaMC

A package for fast downstream analysis of large array comparative genomic…

A package for fast downstream analysis of large array comparative genomic hybridization datasets. VegaMC enables fast and efficient detection of significant recurrent copy number alterations in very…

CNV Workshop
Desktop

CNV Workshop

A suite of software tools and resources for automated, genome-wide CNV…

A suite of software tools and resources for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and…

JISTIC
Desktop

JISTIC

A tool for analyzing datasets of genome-wide copy number variation to identify…

A tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer.

UPDtool
Desktop

UPDtool

A computational tool for detection and classification of uniparental disomy…

A computational tool for detection and classification of uniparental disomy (UPD) in trio SNP-microarray experiments. We were able to detect hetero- and isodisomies from maternal and paternal origin…

StrandScript
Desktop

StrandScript

Converts all genotyping data generated from Illumina genotyping arrays to the…

Converts all genotyping data generated from Illumina genotyping arrays to the reference forward strand. StrandScript works independently of the Illumina array version and is future proof for newer…

MiPP
Desktop

MiPP Misclassification-Penalized Posterior

Assesses the performance of a prediction model. MiPP assesses the sum of the…

Assesses the performance of a prediction model. MiPP assesses the sum of the posterior classification probabilities penalized by the number of incorrectly classified samples. It has shown that the…

maPredictDSC
Desktop

maPredictDSC

Implements the classification pipeline of the best overall team (Team221) in…

Implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. maPredictDSC facilitates the development of microarray-based prediction…

BASH
Desktop

BASH BeadArray Subversion of Harshlight

Adopts the concepts of Harshlight, but implements them in a manner that…

Adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. BASH requires knowledge of the direct neighbours of a bead, and…

ASSIsT
Desktop

ASSIsT Automatic SNP ScorIng Tool

A user-friendly customized pipeline for efficient calling and filtering of SNPs…

A user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated…

PhenogramViz
Desktop

PhenogramViz

Supports phenotype-driven interpretation of aCGH findings based on multiple…

Supports phenotype-driven interpretation of aCGH findings based on multiple data sources, including the integrated cross-species phenotype ontology Uberpheno, in order to visualise gene-to-phenotype…

CNV-WebStore
Web

CNV-WebStore

An online platform to streamline the processing and downstream interpretation…

An online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided…

Copy Number…
Desktop
Web

Copy Number Explorer

An interactive tool for mining large copy number datasets. Copy Number Explorer…

An interactive tool for mining large copy number datasets. Copy Number Explorer facilitates rapid visual and statistical identification of recurrent regions of gain or loss, identifies the genes most…

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