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

canEvolve – Integrative Cancer Genomics analysis of Expression, Copy Number, miRNAs and Network

canEvolve

:: DESCRIPTION

canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets.

::DEVELOPER

CanEvolve Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

canEvolve: a web portal for integrative oncogenomics.
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK.
PLoS One. 2013;8(2):e56228. doi: 10.1371/journal.pone.0056228.

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.

CONSERTING – Copy Number Segmentation by Regression Tree in Next Generation Sequencing

CONSERTING

:: DESCRIPTION

CONSERTING (Copy Number Segmentation by Regression Tree in Next Generation Sequencing) is an accurate method for detecting somatic DNA copy number variation in whole genome sequencing data.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R package

:: DOWNLOAD

 CONSERTING

:: MORE INFORMATION

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.

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.

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.