Tag: Copy Number

Tumorscape 1.6 – Copy Number Alterations Across Multiple Cancer Types

Tumorscape 1.6

:: DESCRIPTION

The Tumorscape portal facilitates the use and understanding of high resolution copy number data amassed from multiple cancer types. It supports gene-level analysis, analysis by cancer type, and the downloading/browsing of data.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M. et al.
The landscape of somatic copy-number alteration across human cancers.
Nature. 2010;463:899–905. doi: 10.1038/nature08822.

BASTA – Bayesian Modeling of DNA copy number amplification data

BASTA

:: DESCRIPTION

BASTA contains an implementation of a Bayesian model-based method for unsupervised classification of tissue samples based on DNA copy number amplifications.

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  BASTA

:: MORE INFORMATION

Citation:

Marttinen, Pekka, Myllykangas, Samuel and Corander, Jukka (2009)
Bayesian clustering and feature selection for cancer tissue samples
BMC Bioinformatics 2009, 10:90

MPCBS 1.1.1 – Multi-platform segmentation for DNA copy number data

MPCBS 1.1.1

:: DESCRIPTION

MPCBS (Multi-Platform Circular Binary Segmentation) is a software which pools statistical evidence across platforms during segmentation, and does not require pre-standardization of different data sources. It involves a weighted sum of t-statistics, which arises naturally from the generalized log-likelihood ratio of a multi-platform model.

::DEVELOPER

Nancy R. Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R Package

:: DOWNLOAD

 MPCBS

:: MORE INFORMATION

Citation

Zhang, NR, Senbabaoglu, Y and Li, J, 2010,
Joint Estimation of DNA Copy Number from Multiple Platforms.
Bioinformatics, 26, 153-160.

PSCN 1.0 – Parent-Specific Copy Number Estimation

PSCN 1.0

:: DESCRIPTION

PSCN segments the genome of a sample into homogeneous parts and gives an estimation of parent-specific DNA copy number using high-density SNP array data (logR and B-allele frequency). This package can be applied on platforms having both SNP probes and copy number probes.

::DEVELOPER

Hao Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R Package

:: DOWNLOAD

  PSCN

:: MORE INFORMATION

Citation

Chen, H., Xing, H. and Zhang, N.R., 2011,
Stochastic segmentation models for allele-specific copy number estimation with SNP-array data,
PLoS Computational Biology, 7, e1001060.

CNAnova 1.0 – Identify Recurrent Regions of Copy Number Changes

CNAnova 1.0

:: DESCRIPTION

CNAnova is a stand-alone software package for identifying recurrent regions of copy number aberrations (CNAs) using SNP microarray data. It runs from the command line on the Linux platforms and is composed of several modules written in the R programming language.

::DEVELOPER

Sergii Ivakhno

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  CNAnova

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Jun 1;26(11):1395-402. Epub 2010 Apr 18.
CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data.
Ivakhno S, Tavaré S.

CnD 1.3 – Copy Number Variant Caller for Inbred Strains

CnD 1.3

:: DESCRIPTION

cnD (Copy number variant detection) is a program to detect copy number variants from short read sequence data.

::DEVELOPER

Jared Simpson (js18@sanger.ac.uk).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  CnD

:: MORE INFORMATION

Citation

Copy number variant detection in inbred strains from short read sequence data.
Simpson JT, McIntyre RE, Adams DJ and Durbin R
Bioinformatics (Oxford, England) 2010;26;4;565-7

STAC 1.2 – Significance Testing for Aberrant Copy-Number

STAC 1.2

:: DESCRIPTION

STAC (Significance Testing for Aberrant Copy-Number) is a method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. It utilizes two complementary statistics in combination with a novel search strategy. The significance of both statistics is assessed, and P-values are assigned to each location on the genome by using a multiple testing corrected permutation approach. STAC identifies genomic alterations known to be of clinical and biological significance and provides statistical support for 85% of previously reported regions. Moreover, STAC identifies numerous additional regions of significant gain/loss in these data that warrant further investigation. The P-values provided by STAC can be used to prioritize regions for follow-up study in an unbiased fashion.

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  •  Java

:: DOWNLOAD

 STAC

:: MORE INFORMATION

Citation:

Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr, Weber BL, Maris JM, Grant GR.
STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
Genome Res. 2006 Sep;16(9):1149-58. Epub 2006 Aug 9.

GMM – Detects Copy Number Variation from the Distribution of Copy Number Ratios

GMM

:: DESCRIPTION

GMM (Gaussian Mixture Model) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage).

::DEVELOPER

Computational Biology Group ,Department of Medical Genetics, University of Lausanne

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  GMM

:: MORE INFORMATION

CNSuite – caBIG Analytical Tool for Copy Number analysis

CNSuite

:: DESCRIPTION

CNSuite (Copy Number Suite) is a caBIGTM (cancer Biomedical Informatics Grid) analytical tool for gene copy number change analysis. CNSuite consists of a Fused Margin Regression (FMR) method for detecting copy number changes in a single signal profile and consensus copy number changes in population data, and two feature indexing methods for analyzing chromosomal instabilities (CIN). CNSuite is applicable to analyzing germline copy number variations (CNV) in the study of population genetics and somatic copy number alterations (CNA) in tumor genomics.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CNSuite

:: MORE INFORMATION

BACOM 1.0 – Bayesian Analysis of COpy number Mixtures

BACOM 1.0

:: DESCRIPTION

BACOM (Bayesian Analysis of COpy number Mixtures) is a statistically-principled in silico approach to accurately estimate genomic deletions and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We have developed a cross-platform and open source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues and other relevant processing steps. We also provide an R interface, bacomR, for running BACOM within the R environment, through which users can smoothly incorporate BACOM into their specific analyses.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BACOM

:: MORE INFORMATION

Citation:

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.
Yu G, Zhang B, Bova GS, Xu J, Shih IeM, Wang Y.
Bioinformatics. 2011 Jun 1;27(11):1473-80. Epub 2011 Apr 15.