DupHMM
:: DESCRIPTION
DupHMM is an easy to use copy number variant identifier
::DEVELOPER
Korf Lab at the University of California, Davis.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows/MacOsX/Linux
- Python
- R package
:: DOWNLOAD
:: MORE INFORMATION
Tag: Copy Number
CNOGpro 1.1 – Copy Numbers of Genes in Prokaryotes
CNOGpro 1.1
:: DESCRIPTION
CNOGpro is a methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms.
::DEVELOPER
Ola Brynildsrud <ola.brynildsrud at nmbu.no>, Lars-Gustav Snipen
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows / MacOsX
- R
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2015 Feb 1. pii: btv070.
CNOGpro: Detection and quantification of CNVs in prokaryotic whole-genome sequencing data.
Brynildsrud O, Snipen LG, Bohlin J
quandico 1.14 – Quantitative Analysis of differences in Copy Numbers
quandico 1.14
:: DESCRIPTION
The tool quandico applies statistical methods to detect copy number variations (CNV) in a sample by comparing the read counts from next generation sequencing (NGS) performed after PCR-enrichment of regions of interest, typically a set of genes with known or expected relevance for the sample, e.g. genes that play a role in cancer. Counts from a normal control (ideally matched normal from the same individual, e.g. healthy tissue) are required.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- R
- Perl
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2015 Jan 28;16(1):17.
Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.
Reinecke F, Satya R, DiCarlo J.
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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- R
:: DOWNLOAD
:: 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.
Copy Number Explorer 1.3 – Interactive Copy Number Analysis for Cancer Genomics
Copy Number Explorer 1.3
:: DESCRIPTION
Copy Number Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes.
Copy Number Explorer online version
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows / MacOsX
- R
- Perl
:: DOWNLOAD
:: MORE INFORMATION
Citation
Interactive analysis of large cancer copy number studies with Copy Number Explorer.
Newman S.
Bioinformatics. 2015 May 7. pii: btv298.
CoNCoS 0.2 – Copy Number Estimation with Controlled Support
CoNCoS 0.2
:: DESCRIPTION
CoNCoS is a tool for researchers concerned with copy number estimation from next-generation sequencing data.It detects copy number aberrations and outputs a list composed of their position, copy number and affected gene(s).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux/ Windows
- JRE
:: DOWNLOAD
:: MORE INFORMATION
Citation
CoNCoS: Copy number estimation in cancer with controlled support.
Abdallah AT, Fischer M, Nürnberg P, Nothnagel M, Frommolt P.
J Bioinform Comput Biol. 2015 Sep 4:1550027.
CopyNumber450kCancer 1.0.4 – Baseline Correction for Copy Number Data from Cancer Samples
CopyNumber450kCancer 1.0.4
:: DESCRIPTION
CopyNumber450kCancer takes the output of CopyNumber450k and ChAMP packages and correct the baseline in each sample for accurate copy number calling, specially in cancer samples. CopyNumber450kCancer can read the segment output file from CopyNumber450k package directly without any need for modification. Output files from ChAMP need to be in one file not in seperated files.
::DEVELOPER
Molecular Medicine research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows
- R
:: DOWNLOAD
:: MORE INFORMATION
Citation
CopyNumber450kCancer: Baseline Correction for Accurate Copy Number Calling from the 450k Methylation Array.
Marzouka NA, Nordlund J, Bäcklin CL, Lönnerholm G, Syvänen AC, Almlöf JC.
Bioinformatics. 2015 Nov 9. pii: btv652
TrioCNV 0.1.2 – Joint Detection of Copy Number Variations in Parent-offspring Trios
TrioCNV 0.1.2
:: DESCRIPTION
TrioCNV is a tool designed to jointly detecting CNVs from WGS data in parent-offspring trios.
::DEVELOPER
yzhuangliu@gmail.com
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / Linux
- R
- JRE
:: DOWNLOAD
:: MORE INFORMATION
Citation
Joint detection of copy number variations in parent-offspring trios.
Liu Y, Liu J, Lu J, Peng J, Juan L, Zhu X, Li B, Wang Y.
Bioinformatics. 2015 Dec 7. pii: btv707.
jointSeg 0.7.0- Joint segmentation of multivariate (copy number) signals
jointSeg 0.7.0
:: DESCRIPTION
The jointSeg R package implements functions to quickly segment multivariate signals into piecewise constant profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies.
::DEVELOPER
Laboratoire de Mathématiques et Modélisation d’Évry
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows/Linux/ MacOsX
- R package
:: DOWNLOAD
:: MORE INFORMATION
Citation
Brief Bioinform. 2014 Sep 8. pii: bbu026.
Performance evaluation of DNA copy number segmentation methods.
Pierre-Jean M, Rigaill G, Neuvial P.
Contra 2.0.8 – Copy Number Analysis for Targeted Resequencing
Contra 2.0.8
:: DESCRIPTION
CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
- Linux / MacOsX /Windows
- Python
- R package
- BEDTools
- SAMtools
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li, et al.
CONTRA: copy number analysis for targeted resequencing
Bioinformatics (2012) 28 (10): 1307-1313.