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CNV identification software tools | Genomic array data analysis

Copy number variants (CNVs) create a major source of variation among individuals and populations. Array-based comparative genomic hybridisation (aCGH) is a powerful method used to detect and compare the copy numbers of DNA sequences at high…
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…

GLAD
Desktop

GLAD Gain and Loss Analysis of DNA

A package for the automatic detection of breakpoints from array CGH profile,…

A package for the automatic detection of breakpoints from array CGH profile, and the assignment of a status to each chromosomal region. The breakpoint detection step of GLAD is based on the Adaptive…

RLMM
Desktop

RLMM

A classification algorithm which uses the robust, multi-chip average (RMA)…

A classification algorithm which uses the robust, multi-chip average (RMA) method to combine the intensities across probes and chips and produce allele-based summaries. This is a supervised learning…

QuantiSNP
Desktop

QuantiSNP

Designed to detect rare or de novo copy number alterations in normal DNA…

Designed to detect rare or de novo copy number alterations in normal DNA samples.

CNVFinder
Desktop

CNVFinder

A tool for accurate and reliable high-throughput detection of copy number…

A tool for accurate and reliable high-throughput detection of copy number variation in the human genome. CNVfinder algorithm was trained using a series of replicate hybridizations of varying quality…

quantsmooth
Desktop

quantsmooth

Quantile smoothing and genomic visualization of array data.

Quantile smoothing and genomic visualization of array data.

cn.FARMS
Desktop

cn.FARMS

A package for array-based CNV (Copy Number Variation) analysis which is…

A package for array-based CNV (Copy Number Variation) analysis which is designed to control the FDR (False Discovery Rate) while ensuring high sensitivity. For controlling the FDR, we propose a…

CRLMM
Desktop

CRLMM

Implements a multilevel model adjusting for batch effects and providing…

Implements a multilevel model adjusting for batch effects and providing allele-specific estimates of copy number. The CRLMM algorithm estimates genotypes through a hierarchical model for the log…

Illuminus
Desktop

Illuminus

A fast and accurate algorithm for assigning single nucleotide polymorphism…

A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology. The algorithm can assign genotypes to…

gsrc
Desktop

gsrc genome structure rearrangement calling

Detects genome structure rearrangements from genotyping data in allopolyploid…

Detects genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. GSRC is a pipeline to read and analyze raw single nucleotide polymorphism…

TriTyper
Desktop

TriTyper

A method that can infer genotypes in case-control data sets for deletion CNVs,…

A method that can infer genotypes in case-control data sets for deletion CNVs, or SNPs with an extra, untyped allele at a high-resolution single SNP level. By accounting for linkage disequilibrium…

RJaCGH
Desktop

RJaCGH Reversible Jump MCMC for the analysis of CGH arrays

Fits a non-homogeneous hidden Markov model to the aCGH data using Markov chain…

Fits a non-homogeneous hidden Markov model to the aCGH data using Markov chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these…

CGHregions
Desktop

CGHregions

Reduces the dimension of array Comparative Genomic Hybridization (CGH) data…

Reduces the dimension of array Comparative Genomic Hybridization (CGH) data while assuring the loss of information. CGHregions is an algorithm implemented using R. It was shown that using the regions…

SNPchip
Desktop

SNPchip

Contains classes and methods useful for storing, visualizing and analyzing high…

Contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open…

optiCall
Desktop

optiCall

A genotype-calling algorithm for Illumina arrays that uses both SNP-wise and…

A genotype-calling algorithm for Illumina arrays that uses both SNP-wise and sample-wise calling to more accurately ascertain genotypes at rare, low-frequency and common variants, even when genotype…

SNiPer-HD
Desktop

SNiPer-HD

Improved genotype calling accuracy by an expectation-maximization algorithm for…

Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.

CGHweb
Web

CGHweb

A web-based tool that applies a number of popular algorithms to a single array…

A web-based tool that applies a number of popular algorithms to a single array CGH profile entered by the user. CGHweb generates a heatmap panel of the segmented profiles for each method as well as a…

ALCHEMY
Desktop

ALCHEMY

A method for automated calling of diploid genotypes from raw intensity data…

A method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods.

AS-GENSENG
Desktop

AS-GENSENG

Incorporates allele-specific read counts in CNV detection and estimates…

Incorporates allele-specific read counts in CNV detection and estimates accurate allele-specific copy number (ASCN) using either WGS or WES data. AS-GENSENG not only predicts ASCN calls but also…

pennCNV_Pipelin…
Desktop

pennCNV_Pipeline

A quality score for copy number variants (CNVs) detected by PennCNV, prior to…

A quality score for copy number variants (CNVs) detected by PennCNV, prior to performing CNV-based association studies. Our contribution can be viewed as a post-processing step of PennCNV calls,…

Ultrasome
Desktop

Ultrasome

An efficient methodology for detecting and delineating gains and losses of…

An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.

CNVDetector
Desktop

CNVDetector

A program for locating copy number variations in a single genome using array…

A program for locating copy number variations in a single genome using array CGH data.

CGHPRO
Desktop

CGHPRO

Allows to analyze and visualize array comparative genomic hybridisation (CGH)…

Allows to analyze and visualize array comparative genomic hybridisation (CGH) data. CGHPRO is a standalone application that features the test of hybridization quality, normalization and…

SnoopCGH
Desktop

SnoopCGH

SnoopCGH is a java desktop application for visualising and exploring…

SnoopCGH is a java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

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…

MD-SeeGH
Desktop

MD-SeeGH

A platform for the integrative analysis of diverse microarray data,…

A platform for the integrative analysis of diverse microarray data, facilitating multiple profile analyses and group comparisons.

SCIMMkit
Desktop

SCIMMkit

An integrated toolkit for targeted CNV detection and genotyping using Illumina…

An integrated toolkit for targeted CNV detection and genotyping using Illumina Infinium II and GoldenGate BeadXpress assays.

CNVCALL
Desktop

CNVCALL

Identifies both the number of different copy number classes at a specific locus…

Identifies both the number of different copy number classes at a specific locus as well as relative copy number for each individual in the sample.

HaMMLET
Desktop

HaMMLET

A fast forward-backward Gibbs sampler for Bayesian inference on hidden Markov…

A fast forward-backward Gibbs sampler for Bayesian inference on hidden Markov models (HMM). HaMMLET uses the Haar wavelet transform to dynamically compress the data based on the current variance…

iCall
Desktop

iCall

An improved genotype-calling algorithm for rare and common variants on the…

An improved genotype-calling algorithm for rare and common variants on the Illumina exome array.

affy2sv
Desktop

affy2sv

An R package to pre-process raw .CEL files from Affymetrix CytoScan HD and 750k…

An R package to pre-process raw .CEL files from Affymetrix CytoScan HD and 750k arrays (also the old SNP arrays called Genome-Wide SNP 5.0/6.0 and Axiom). The package can be used to create a wide…

SubPatCNV
Desktop

SubPatCNV Subspace Pattern-ming of Copy Number Variations

A data mining tool for discovery of CNV regions that exhibit in subsets of…

A data mining tool for discovery of CNV regions that exhibit in subsets of samples larger than a support threshold. SubPatCNV is suitable for analysis of arrayCGH data of a population or a patient…

G T A T C G C T A
ViVar
Web

ViVar

A comprehensive analysis platform for the processing, analysis and…

A comprehensive analysis platform for the processing, analysis and visualization of structural variation based on sequencing data or genomic microarrays, enabling the rapid identification of disease…

GStream
Desktop

GStream

Provides a high performance in genotyping accuracy when analyzing Genome-Wide…

Provides a high performance in genotyping accuracy when analyzing Genome-Wide Association Studies (GWAS) data from Illumina BeadChip arrays. GStream is a method for Single Nucleotide Polymorphisms…

Rawcopy
Desktop

Rawcopy

An R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP…

An R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). Rawcopy uses data from a large number of reference samples to produce log…

VanillaICE
Desktop

VanillaICE

Uses Hidden Markov Models (HMM) for characterizing chromosomal alterations in…

Uses Hidden Markov Models (HMM) for characterizing chromosomal alterations in high throughput SNP arrays. VanillaICE provides a simple interface for fitting HMMs and plotting functions to help…

SMAP
Desktop

SMAP A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

Provides functions and classes for DNA copy number profiling of Comparative…

Provides functions and classes for DNA copy number profiling of Comparative Genomic Hybridization (CGH) data. SMAP is a segmental maximum a posteriori approach to array-CGH copy number profiling.…

mBPCR
Desktop

mBPCR

A package that estimates the DNA copy number profile using mBPCR to detect…

A package that estimates the DNA copy number profile using mBPCR to detect regions with copy number changes.

MinimumDistance
Desktop

MinimumDistance

A package for the analysis of de novo copy number variants in trios from…

A package for the analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

beadarraySNP
Desktop

beadarraySNP

Importing data from Illumina SNP experiments and performing copy number…

Importing data from Illumina SNP experiments and performing copy number calculations and reports.

BRLMM
Desktop

BRLMM

An Improved Genotype Calling Method for the GeneChip Human Mapping 500K Array…

An Improved Genotype Calling Method for the GeneChip Human Mapping 500K Array Set.

BRLMM-P
Desktop

BRLMM-P

A Genotype Calling Method for the SNP 5.0 Array. BRLMM-P derives seed genotypes…

A Genotype Calling Method for the SNP 5.0 Array. BRLMM-P derives seed genotypes directly from the clustering properties of the data and performs a multiple chip analysis, enabling the simultaneous…

BCRgt
Desktop
Genovar
Desktop

Genovar

Detects copy number variation (CNV) regions and provides a visual inspection…

Detects copy number variation (CNV) regions and provides a visual inspection function to reduce false positive CNV calls based on comparative genomic hybridization arrays (aCGH) and next generation…

Birdseed
Desktop

Birdseed

A SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0…

A SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms.

ISACGH
Desktop

ISACGH In Silico Array-CGH

Allows visualizing array CGH data or/and expression arrays onto human or mouse…

Allows visualizing array CGH data or/and expression arrays onto human or mouse chromosomal coordinates (automatically found through their standard identifiers) and represents the regions with copy…

GenoSNP
Desktop

GenoSNP

Allows genotype calling for the Illumina Infinium single nucleotide…

Allows genotype calling for the Illumina Infinium single nucleotide polymorphism (SNP) genotyping array. GenoSNP can call genotypes within-sample. The within-sample genotyping capability is…

CNIT
Desktop

CNIT Copy Number Inferring Tool

Determines single nucleotide polymorphism (SNP) allelic copy number (CN) and to…

Determines single nucleotide polymorphism (SNP) allelic copy number (CN) and to investigate subtle alterations in chromosomal structures. CNIT employs the hidden Markov model (HMM) method to identify…

CGcgh
Desktop
CGHAnalyzer
Desktop

CGHAnalyzer

Provides an overview of array-based comparative genomic hybridization data…

Provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this purpose. CGHAnalyzer…

SNPolisher
Desktop

SNPolisher

An R package for post-process analyses of Affymetrix Axiom Genotyping Arrays…

An R package for post-process analyses of Affymetrix Axiom Genotyping Arrays results.

Gencall
Desktop

Gencall

Software algorithms for clustering, calling, and scoring genotypes.

Software algorithms for clustering, calling, and scoring genotypes.

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