Tag: Copy Number

DANCE 0.99.0 – Deregulation of Copy-number and Expression

DANCE 0.99.0

:: DESCRIPTION

DANCE quantifies the impact of copy-number alterations on gene expression and compares it between tumour sub-types.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

 DANCE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.
Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.
Yuan Y1, Rueda OM, Curtis C, Markowetz F.

MEDICC – Minimum Event Distance for Intra-tumour Copy number Comparisons

MEDICC

:: DESCRIPTION

MEDICC harnesses the power of a finite-state automaton representation of genomic profiles to model genomic rearrangement events with horizontal dependencies.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

 MEDICC

:: MORE INFORMATION

Citation

Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F.
PLoS Comput Biol. 2014 Apr 17;10(4):e1003535. doi: 10.1371/journal.pcbi.1003535

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.

IgC2N – Identification of Germline Changes in Copy Number

IgC2N

:: DESCRIPTION

IgC2N is a three step computational framework to discover and genotype germline CNVs

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOSX
  • R

:: DOWNLOAD

  IgC2N

:: MORE INFORMATION

Citation:

PLoS One. 2011 Mar 29;6(3):e17539. doi: 10.1371/journal.pone.0017539.
A computational framework discovers new copy number variants with functional importance.
Banerjee S1, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F.

cn.FARMS 1.34.0 – Factor Analysis for Copy Number Estimation

cn.FARMS 1.34.0

:: DESCRIPTION

cn.FARMS is a latent variable model for detecting copy number variations in microarray data.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R Package
  • BioConductor

:: DOWNLOAD

 cn.FARMS

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(12):e79. doi: 10.1093/nar/gkr197. Epub 2011 Apr 12.
cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate.
Clevert DA1, Mitterecker A, Mayr A, Klambauer G, Tuefferd M, De Bondt A, Talloen W, G?hlmann H, Hochreiter S.

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.

mrCaNaVaR 0.51 – Micro-read Copy Number Variant Regions

mrCaNaVaR 0.51

:: DESCRIPTION

mrCaNaVaR is a copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

::DEVELOPER

Can Alkan 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mrCaNaVaR

:: MORE INFORMATION

Citation

Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, Evan E. Eichler.
Personalized copy number and segmental duplication maps using next-generation sequencing.
Nature Genetics, Oct, 41(10):1061-1067, 2009.

DLMM 0.0.2 – Double-layered Mixture Model for Joint Analysis of Copy Number and Gene Expression Data

DLMM 0.0.2

:: DESCRIPTION

DLMM (Double-layered Mixture Model) is a software to select copy number-associated gene expression changes in high-throughput genomics data. Copy number segmentation results and criterion-based gene selection are separately reported.

::DEVELOPER

Hyungwon Choi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

  DLMM

:: MORE INFORMATION

Citation:

H. Choi, Z.S. Qin, and D. Ghosh (2010),
A Double-layered Mixture Model for Joint Analysis of Copy Number and Gene Expression Data.
J. Comput. Biol. 17(2):1-17.

SimCopy 0.2 – Simulate the Evolution of Copy Number Profiles along a Tree

SimCopy 0.2

:: DESCRIPTION

SimCopy is an R package simulating the evolution of copy number profiles along a tree. It relies on the PhyloSim package for performing the simulations by encoding the genomic regions as sites in sequences and using modified processes acting on them.

::DEVELOPER

Botond Sipos

:: REQUIREMENTS

:: DOWNLOAD

 SimCopy

:: MORE INFORMATION

ABSOLUTE 1.0 / HAPSEG – Estimate Purity/Ploidy and absolute copy-number and mutation data

ABSOLUTE 1.0 / HAPSEG

:: DESCRIPTION

The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.

HAPSEG is a probabilistic method to interpret bi- allelic marker data in cancer samples.

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ABSOLUTE , HAPSEG

:: MORE INFORMATION

Citation

Scott L Carter, et cl.
Absolute quantification of somatic DNA alterations in human cancer
Nature Biotechnology 30, 413–421 (2012) doi:10.1038/nbt.2203

Scott L. Carter, Matthew Meyerson & Gad Getz
Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping