AmpliCoNE – Ampliconic Copy Number Estimator

AmpliCoNE

:: DESCRIPTION

AmpliCoNE is a tool to estimate the copy number of ampliconic gene families in human Y chromosome using Illumina whole genome sequencing data.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

AmpliCoNE

:: MORE INFORMATION

Citation

PLoS Genet, 15 (9), e1008369 2019 Sep 16 eCollection Sep 2019
Dosage Regulation, and Variation in Gene Expression and Copy Number of Human Y Chromosome Ampliconic Genes
Rahulsimham Vegesna , Marta Tomaszkiewicz, Paul Medvedev, Kateryna D Makova

Reprever 0.1.1 – Find and Reconstruct Extra Copies given Copy Number Gain Regions

Reprever 0.1.1

:: DESCRIPTION

Reprever (REPeat REsolVER) finds and reconstructs extra copies given copy number gain regions.

::DEVELOPER

Sangwoo Kim

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Java

:: DOWNLOAD

  Reprever

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 May 8. [Epub ahead of print]
Reprever: resolving low-copy duplicated sequences using template driven assembly.
Kim S, Medvedev P, Paton TA, Bafna V.

CNVer 0.8.1 – method for Detecting Copy Number Variation

CNVer 0.8.1

:: DESCRIPTION

CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 CNVer

:: MORE INFORMATION

Citation

Genome Res. 2010 Nov;20(11):1613-22. doi: 10.1101/gr.106344.110. Epub 2010 Aug 30.
Detecting copy number variation with mated short reads.
Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M.

fCNV – Detecting Copy Number Variation in a Fetal Genome

fCNV

:: DESCRIPTION

fCNV is a probabilistic method for non-invasive analysis of de novo CNVs in fetal genome based on maternal plasma sequencing

::DEVELOPER

Computational Biology Lab at the University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Python

:: DOWNLOAD

 fCNV

:: MORE INFORMATION

Citation:

Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing.
Rampášek L, Arbabi A, Brudno M.
Bioinformatics. 2014 Jun 15;30(12):i212-i218. doi: 10.1093/bioinformatics/btu292.

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.