AVAtar 0.4.11 – Analysis and Visualization of Alteration data

AVAtar 0.4.11

:: DESCRIPTION

Avatar features interactively customizable alteration plots, extensive data import capabilities and a multi-objective optimization algorithm to find alteration patterns, e.g. gene sets with mutually exclusive alterations or small gene sets with high sample coverage.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

AVAtar

:: MORE INFORMATION

Citation

Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffman TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA.
Analysis, identification and visualization of subgroups in genomics.
Brief Bioinform. 2021 May 20;22(3):bbaa217. doi: 10.1093/bib/bbaa217. Erratum in: Brief Bioinform. 2021 Jul 06;: PMID: 32954413; PMCID: PMC8138884.

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 Park’s lab at CBMI, Harvard Medical School

:: 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.

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.

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.