Tag: Aberration

ReadDepth 0.9.8.4 – Detects Copy Number Aberrations in Deep Sequencing Data

ReadDepth 0.9.8.4

:: DESCRIPTION

The readDepth package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. It achieves higher accuracy than many other packages, and runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets.

::DEVELOPER

the Bioinformatics Research Laboratory at Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 ReadDepth

:: MORE INFORMATION

Citation

Miller CA, Hampton O, Coarfa C, Milosavljevic A, 2011
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads.
PLoS ONE 6(1): e16327. doi:10.1371/journal.pone.0016327

ADTEx 2.0 – Aberration Detection in Tumour Exome

ADTEx 2.0

:: DESCRIPTION

ADTEx is a freely available software package coded using R statistical language and Python to detect somatic copy number variations (CNVs) and genotypes in tumour whole exome samples. ADTEx is suitable for paired tumour/matched normal samples.

::DEVELOPER

Kaushalya Amarasinghe <kaushalya.amarasinghe@unimelb.edu.au>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python
  • BedTOol

:: DOWNLOAD

 ADTEx

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 Aug 28;15:732. doi: 10.1186/1471-2164-15-732.
Inferring copy number and genotype in tumour exome data.
Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK

CARMA 1.0 – Copy Aberration Regional Mapping Analysis

CARMA 1.0

:: DESCRIPTION

CARMA is a computational tool to analyse allele-specific copy number profiles from tumor DNA obtained with SNP arrays or by high-throughput sequencing.

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 CARMA

:: MORE INFORMATION

Citation:

Dissecting genome aberration patterns in tumors,
Nilsen et al. 2014 (manuscript)

RAIG 1.0.2 – Identifying Recurrent and Independent Copy Number Aberration

RAIG 1.0.2

:: DESCRIPTION

RAIG ( Recurrent Aberrations from Interval Graph) is a combinatorial approach to the problem of identifying independent and recurrent copy number aberrations, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 RAIG

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jun 15;30(12):i195-i203. doi: 10.1093/bioinformatics/btu276.
Detecting independent and recurrent copy number aberrations using interval graphs.
Wu HT, Hajirasouliha I, Raphael BJ.

DiNAMIC – Identify recurrent DNA copy number Aberrations in Tumors

DiNAMIC

:: DESCRIPTION

DiNAMIC (Discovering Copy Number Aberrations Manifested In Cancer) is a novel method for assessing the statistical significance of recurrent copy number aberrations. In contrast to competing procedures, the testing procedure underlying DiNAMIC is carefully motivated, and employs a novel cyclic permutation scheme. Extensive simulation studies show that DiNAMIC controls false positive discoveries in a variety of realistic scenarios.

::DEVELOPER

V. Walter, A.B. Nobel, and F.A. Wright

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 DiNAMIC

:: MORE INFORMATION

Citation

V. Walter, A.B. Nobel, and F.A. Wright
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
Bioinformatics (2011) 27 (5): 678-685.