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Somatic CNA identification software tools | Genomic array data analysis

DNA copy number aberration (CNA) is very important in the pathogenesis of tumors and other diseases. For example, CNAs may result in suppression of anti-oncogenes and activation of oncogenes, which would cause certain types of cancers. High density…
ASCAT
Desktop

ASCAT

A tool for accurate dissection of genome-wide allele-specific copy number in…

A tool for accurate dissection of genome-wide allele-specific copy number in tumors.

GISTIC
Desktop

GISTIC

Methods with enhanced power and specificity to identify genes targeted by…

Methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth.

CGHcall
Desktop

CGHcall

Achieves high calling accuracy for array CGH data by effective use of…

Achieves high calling accuracy for array CGH data by effective use of breakpoint information from segmentation and by inclusion of several biological concepts that are ignored by existing algorithms.…

GAP
Desktop

GAP Genome Alteration Print

A method for automatic detection of absolute segmental copy numbers and…

A method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by SNP arrays.

OncoSNP
Desktop

OncoSNP

An analytical tool for characterising copy number alterations and…

An analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data.

GenoCN
Desktop

GenoCN

A software that simultaneously identify copy number states and genotype calls.

A software that simultaneously identify copy number states and genotype calls.

ADaCGH
Desktop
Web

ADaCGH Analysis of Data from aCGH

A web tool for the analysis of aCGH data sets. ADaCGH is a package that…

A web tool for the analysis of aCGH data sets. ADaCGH is a package that parallelizes the main segmentation algorithms (using forking on multicore computers or parallelization via message passing…

TAPS
Desktop

TAPS Tumor Aberration Prediction Suite

A bioinformatic tool for the identification of allele-specific copy numbers in…

A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays.

GPHMM
Desktop

GPHMM

A statistical method dedicated to identify copy number alteration and loss of…

A statistical method dedicated to identify copy number alteration and loss of heterozygosity (LOH) in tumor samples using whole genome SNP arrays.

CNARA
Desktop

CNARA Copy Number Alterations Reliability Assessment

A method for the assessment of genomic copy number profiling data. CNARA could…

A method for the assessment of genomic copy number profiling data. CNARA could be instrumental in improving the assessment of data used for genomic data mining experiments and support the reliable…

CMDS
Desktop

CMDS

A population-based method for DNA copy number analysis: recurrent copy number…

A population-based method for DNA copy number analysis: recurrent copy number aberration identification in multiple samples (with no need of single-sample calling).

DiNAMIC
Desktop
PLA
Desktop

PLA

A general and robust method to identify recurrent CNVs from multi-sample aCGH…

A general and robust method to identify recurrent CNVs from multi-sample aCGH profiles.

CGARS
Desktop

CGARS Cancer Genome Analysis by Rank Sums

A method to dissect random from non-random patterns in copy number data and…

A method to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell…

CNAnova
Desktop

CNAnova

A stand-alone software package for identifying recurrent regions of copy number…

A stand-alone software package for identifying recurrent regions of copy number aberrations (CNAs) using SNP microarray data.

SLM
Desktop

SLM Shifting Level Model

Detects genetic changes that involve gain or loss of segments of genomic DNA…

Detects genetic changes that involve gain or loss of segments of genomic DNA from array comparative genomic hybridization (aCGH) data. SLM is an algorithm that allows user to simulate noisy…

FastCall
Algorithm

FastCall

Allows classification of each region of segmented array comparative genomic…

Allows classification of each region of segmented array comparative genomic hybridization (aCGH) data. FastCall offers user to separate region into 3/4 biologically motivated states. This algorithm…

WIFA
Desktop

WIFA Wavelet-based Identification of Focal genomic Aberrations

Allows detection of broad and focal aberrations in single nucleotide…

Allows detection of broad and focal aberrations in single nucleotide polymorphism SNP array data sets. WIFA can (i) distinguish signals from noise among probes having high aberrations, (ii) detect…

RAIG
Desktop

RAIG Recurrent Aberrations from Interval Graphs

A combinatorial approach to the problem of identifying independent and…

A combinatorial approach to the problem of identifying independent and recurrent copy number aberrations, focusing on the key challenging of separating the overlaps in aberrations across individuals…

Clonality
Desktop

Clonality

Statistical tests for clonality versus independence of tumors from the same…

Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles.

ASP
Desktop

ASP Autocorrelation Scanning Profile

A mathematical tool to find repeating patterns in time series data to and to…

A mathematical tool to find repeating patterns in time series data to and to assess the dependence of measurement error between neighboring probes. ASP has the following appealing properties: (i) the…

PennCNV-tumor
Desktop

PennCNV-tumor

A software tool for fast and accurate CNA detection using signal intensity data…

A software tool for fast and accurate CNA detection using signal intensity data from SNP genotyping arrays. PennCNV-tumor is an HMM-based method that is loosely based on the model used in PennCNV, an…

CRP_CNV
Desktop

CRP_CNV

A conditional random pattern (CRP) model for CNA detection where much…

A conditional random pattern (CRP) model for CNA detection where much contextual cues are explored to suppress the noise and improve CNA detection accuracy. The proposed CRP model could effectively…

PICNIC
Desktop

PICNIC Predicting Integral Copy Numbers In Cancer

An algorithm designed to identify copy number segments and genotypes in cancer…

An algorithm designed to identify copy number segments and genotypes in cancer using a SNP6 'cel' file as input. Although using generalized copy number software upon cancer data can lead to…

MixHMM
Desktop

MixHMM

A hidden Markov model using hidden states based on chromosomal structural…

A hidden Markov model using hidden states based on chromosomal structural aberrations.

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…

FACADE
Desktop

FACADE Fast Algorithm for Calling After Detection of Edges

A rapid segmentation and calling algorithm that performs competitively with…

A rapid segmentation and calling algorithm that performs competitively with other popular algorithms, while demonstrating rapid execution times which can be orders of magnitude faster than…

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