VanillaICE 1.46.0 – Hidden Markov model for inferring Copy Number Alterations from SNP Arrays

VanillaICE  1.46.0

:: DESCRIPTION

VanillaICE is a Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 VanillaICE

:: MORE INFORMATION

Citation

Ann Appl Stat. 2008 Jun 1;2(2):687-713.
Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.
Scharpf RB1, Parmigiani G, Pevsner J, Ruczinski I.

MOCSphaser – Infer Haplotypes composed of Copy Numbers Alleles and SNP Alleles

MOCSphaser

:: DESCRIPTION

MOCSphaser is a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 MOCSphaser

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1645-6. doi: 10.1093/bioinformatics/btn242. Epub 2008 May 20.
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
Kato M1, Nakamura Y, Tsunoda T.

crlmm 1.42.0 – Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

crlmm 1.42.0

:: DESCRIPTION

The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number.

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 crlmm

:: MORE INFORMATION

Citation

J Stat Softw. 2011 May 1;40(12):1-32.
Using the R Package crlmm for Genotyping and Copy Number Estimation.
Scharpf RB1, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I.

CalMaTe 0.12.1 – Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

CalMaTe 0.12.1

:: DESCRIPTION

CalMaTe is a multi-array post-processing method of allele-specific copy-number estimates (ASCNs).

::DEVELOPER

Henrik Bengtsson <henrikb at braju.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 CalMaTe

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1793-4. doi: 10.1093/bioinformatics/bts248. Epub 2012 May 9.
CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.
Ortiz-Estevez M1, Aramburu A, Bengtsson H, Neuvial P, Rubio A.

PyLOH 1.4.3 – Discovering Copy Number Variations in Cancer Genomes

PyLOH 1.4.3

:: DESCRIPTION

PyLOH is a tool for discovering copy number variations in cancer genomes

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python

:: DOWNLOAD

  PyLOH

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 21.
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.
Li Y1, Xie X.

copynumber 1.12.0 – Segmentation of Single- and multi-track Copy Number data by penalized least Squares Regression

copynumber 1.12.0

:: DESCRIPTION
The R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioCOnductor

:: DOWNLOAD

 copynumber

:: MORE INFORMATION

Citation:

BMC Genomics. 2012 Nov 4;13:591. doi: 10.1186/1471-2164-13-591.
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.
Nilsen G1, Liestøl K, Van Loo P, Moen Vollan HK, Eide MB, Rueda OM, Chin SF, Russell R, Baumbusch LO, Caldas C, Børresen-Dale AL, Lingjaerde OC.

ASCAT 2.4.3 – Allele-Specific Copy number Analysis of Tumours

ASCAT 2.4.3

:: DESCRIPTION

ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy.

::DEVELOPER

Peter Van Loo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 ASCAT

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13.
Allele-specific copy number analysis of tumors.
Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN.

ONCOCNV 6.5 – Detection of Copy Number Changes in Deep Sequencing data

ONCOCNV 6.5

:: DESCRIPTION

ONCOCNV is a package to detect copy number changes in Deep Sequencing data developed by OncoDNA

::DEVELOPER

OncoDNA , Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R
  • Perl
  • SAMtools

:: DOWNLOAD

 ONCOCNV

:: MORE INFORMATION

Citation

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Frio TR, Hupé P, Barillot E, Laes JF.
Bioinformatics. 2014 Jul 12. pii: btu436.

CONAN 1.1.0 – Copy Number Variation Analysis Software

CONAN 1.1.0

:: DESCRIPTION

CONAN is a freely available client-server software solution which provides an intuitive graphical user interface for categorizing, analyzing and associating CNVs with phenotypes.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

CONAN

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 CONAN

:: MORE INFORMATION

Citation

CONAN: copy number variation analysis software for genome-wide association studies.
Forer L, Schönherr S, Weissensteiner H, Haider F, Kluckner T, Gieger C, Wichmann HE, Specht G, Kronenberg F, Kloss-Brandstätter A.
BMC Bioinformatics. 2010 Jun 14;11:318. doi: 10.1186/1471-2105-11-318.

Contra 2.0.8 – Copy Number Analysis for Targeted Resequencing

Contra 2.0.8

:: DESCRIPTION

CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

::DEVELOPER

Jason Li

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX  /Windows
  • Python
  • R package
  • BEDTools
  • SAMtools

:: DOWNLOAD

 Contra

:: MORE INFORMATION

Citation

Li, et al.
CONTRA: copy number analysis for targeted resequencing
Bioinformatics (2012) 28 (10): 1307-1313.