CNALR 1.0 – Stratification of Tumour Subtypes based on Copy Number Alteration Profiles

CNALR 1.0

:: DESCRIPTION

CNALR is an R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. This webpage is currently set to support the submission of the manuscript Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data

::DEVELOPER

Arief Gusnanto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 CNALR

:: MORE INFORMATION

Citation

Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data.
Gusnanto A, Tcherveniakov P, Shuweihdi F, Samman M, Rabbitts P, Wood HM.
Bioinformatics. 2015 Apr 5. pii: btv191.

HMMcopy 0.1.1 – HMM for Detecting Somatic Copy Number alterations in tumour-normal paired Whole Genome Sequencing data

HMMcopy 0.1.1

:: DESCRIPTION

HMMcopy is a suite of tools to make copy number estimations for whole genome data with GC and mappability correction, then segment and classify copy number profiles with a robust Hidden Markov Model. Designed to work with high coverage whole genome HTS data, it can derive copy number estimations from large (~250GB) aligned BAM files in 2 hours on a single core with minimal memory requirements.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

 HMMcopy

:: MORE INFORMATION

Citation

G. Ha, A. Roth, D. Lai, A. Bashashati, J. Ding, R. Goya, R. Giuliany, J. Rosner, A. Oloumi, K. Shumansky, S.-F. Chin, G. Turashvili, M. Hirst, C. Caldas, M. A. Marra, S. Aparicio, S. P. Shah.
Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer.
Genome Research 2012 Oct;22(10):1995-2007.

CLImAT 1.2.2 – Detection of Copy Number Alteration and Loss of Heterozygosity

CLImAT 1.2.2

:: DESCRIPTION

CLImAT (CNA and LOH Assessment in Impure and Aneuploid Tumors) is a bioinformatic tool for identification of genome-wide aberrations from tumor samples using whole-genome sequencing data.

::DEVELOPER

HI_Lab @ USTC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Matlab

:: DOWNLOAD

 CLImAT

:: MORE INFORMATION

Citation:

CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data.
Yu Z, Liu Y, Shen Y, Wang M, Li A.
Bioinformatics. 2014 Sep 15;30(18):2576-83. doi: 10.1093/bioinformatics/btu346.

Shimmer 0.2 – Detection of genetic Alterations in Tumors using Next-generation Sequence data

Shimmer 0.2

:: DESCRIPTION

Shimmer is a software package for the characterization of genetic differences between two very similar samples, e.g., a tumor sample and its matched normal tissue sample.

::DEVELOPER

NHGRI (the National Human Genome Research Institute)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • samtools
  • R package

:: DOWNLOAD

 Shimmer

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jun 15;29(12):1498-503. doi: 10.1093/bioinformatics/btt183. Epub 2013 Apr 24.
Shimmer: detection of genetic alterations in tumors using next-generation sequence data.
Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC.

VanillaICE 1.52.0 – Hidden Markov model for inferring Copy Number Alterations from SNP Arrays

VanillaICE  1.52.0

:: 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.

rSW-seq – Detection of Copy Number Alterations in Deep Sequencing data

rSW-seq

:: DESCRIPTION

rSW-seq is designed to identify copy number alterations between tumor-vs-matched normal genomes (or between normal-vs-normal genomes for CNV detection) from deep sequencing data generated by next-generation sequencing.  Compared to other algorithms (BreakDancer or MoDIL) using PEM (paired-end mapping) signatures, rSW-seq uses ‘read-depth’ as primary measure, which can be applied to single-end sequencing read set.

::DEVELOPER

Tae-Min Kim. , Peter J.Park

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 rSW-seq

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Aug 18;11:432.
rSW-seq: algorithm for detection of copy number alterations in deep sequencing data.
Kim TM, Luquette LJ, Xi R, Park PJ.

Tumorscape 1.6 – Copy Number Alterations Across Multiple Cancer Types

Tumorscape 1.6

:: DESCRIPTION

The Tumorscape portal facilitates the use and understanding of high resolution copy number data amassed from multiple cancer types. It supports gene-level analysis, analysis by cancer type, and the downloading/browsing of data.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M. et al.
The landscape of somatic copy-number alteration across human cancers.
Nature. 2010;463:899–905. doi: 10.1038/nature08822.