CoNVaQ 0.1.3 – Copy Number Variation-based Association tudies

CoNVaQ 0.1.3

:: DESCRIPTION

CoNVaQ is a web service for CNV-based association study between two or more sample groups.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

CoNVaQ

:: MORE INFORMATION

Citation

BMC Genomics. 2018 May 18;19(1):369. doi: 10.1186/s12864-018-4732-8.
CoNVaQ: a web tool for copy number variation-based association studies.
Larsen SJ, do Canto LM, Rogatto SR, Baumbach J.

cn.MOPS 1.32.0 – Mixture Of PoissonS for Discovering Copy Number variations in Next Generation Sequencing data

cn.MOPS 1.32.0

:: DESCRIPTION

cn.MOPS is an algorithm that accurately detects copy number variations in next generation sequencing data in a study of multiple samples.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R Package
  • BioConductor

:: DOWNLOAD

 cn.MOPS

:: MORE INFORMATION

Citation

Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter.
cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate.
Nucleic Acids Research 2012 40(2)

Magnolya 0.15 – Detection of Copy Number Variation

Magnolya 0.15

:: DESCRIPTION

Magnolya is an algorithm for de novo detection of copy number variation. Magnolya directly compares two next-generation sequencing datasets.

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 Magnolya

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 9. [Epub ahead of print]
De novo detection of copy number variation by co-assembly.
Nijkamp JF, van den Broek MA, Geertman JM, Reinders MJ, Daran JM, de Ridder D.

Ginkgo – Cloud-based Single-cell Copy-number Variation Analysis tool

Ginkgo

:: DESCRIPTION

Ginkgo is a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs).

::DEVELOPER

Robert Aboukhalil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Ginkgo

:: MORE INFORMATION

Citation

Interactive analysis and assessment of single-cell copy-number variations.
Garvin T, Aboukhalil R, Kendall J, Baslan T, Atwal GS, Hicks J, Wigler M, Schatz MC.
Nat Methods. 2015 Nov;12(11):1058-60. doi: 10.1038/nmeth.3578.

DeAnnCNV – Detection and Annotation of Copy Number Variations from Whole-exome Sequencing data

DeAnnCNV

:: DESCRIPTION

DeAnnCNV, an online tool, designed for precise Detection and Annotation of Copy Number Variations (CNVs) from whole-exome sequencing (WES) data.

::DEVELOPER

BioStaCs group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data.
Zhang Y, Yu Z, Ban R, Zhang H, Iqbal F, Zhao A, Li A, Shi Q.
Nucleic Acids Res. 2015 May 26. pii: gkv556.

CNV_SS – Copy Number Variation using Sacle Space

CNV_SS

:: DESCRIPTION

CNV_SS detects CNVs using scale-space filtering. The software is enabling the detection of the types and the exact locations of CNVs of all sizes.

::DEVELOPER

Jeehee Yoon (jhyoon@hallym.ac.kr) and Baeksop Kim (bskim@hallym.ac.kr) @ Database Laboratory, Department of Computer Engineering, Hallym University

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • MatLab

:: DOWNLOAD

 CNV_SS

:: MORE INFORMATION

Citation

A computational method for detecting copy number variations using scale-space filtering.
Lee J, Lee U, Kim B, Yoon J.
BMC Bioinformatics. 2013 Feb 18;14:57. doi: 10.1186/1471-2105-14-57.

BMC Bioinformatics. 2013 Feb 18;14(1):57.
A computational method for detecting copy number variations using scale-space filtering.
Lee J, Lee U, Kim B, Yoon J.

PennCNV 2 20131206 – Copy Number Variation detection

PennCNV 2 20131206

:: DESCRIPTION

PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

PennCNV-2 is the second major release of the popular program PennCNV, which was originally designed for inferring copy number variation in germline DNA using data from genotyping microarrays. PennCNV-2 now supports inference of copy number abberrations in tumor cells (PennCNV-tumor).

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / MacOSX
  • Perl

:: DOWNLOAD

 PennCNV

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 1;29(23):2964-70. doi: 10.1093/bioinformatics/btt521. Epub 2013 Sep 9.
Precise inference of copy number alterations in tumor samples from SNP arrays.
Chen GK1, Chang X, Curtis C, Wang K.

Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S, Hakonarson H, Bucan M.
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
Genome Research 17:1665-1674, 2007

CNVannotator 20131114 – Annotation Server for Copy Number Variation (CNV) in Humans

CNVannotator 20131114

:: DESCRIPTION

CNVannotator is a web server that accepts an input set of human genomic positions in a user-friendly tabular format.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory, Vanderbilt University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2013 Nov 14;8(11):e80170. doi: 10.1371/journal.pone.0080170. eCollection 2013.
CNVannotator: a comprehensive annotation server for copy number variation in the human genome.
Zhao M1, Zhao Z.

CNV Workshop 2.0.11 – Analyzing Genome Variation such as Copy Number Variation (CNV)

CNV Workshop 2.0.11

:: DESCRIPTION

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV).

::DEVELOPER

The Center for Biomedical Informatics (CBMi)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 CNV Workshop

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Feb 4;11:74. doi: 10.1186/1471-2105-11-74.
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.
Gai X1, Perin JC, Murphy K, O’Hara R, D’arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS.

JointSLM 0.1 – Detect Recurrent Copy Number Variations in Depth of Coverage data

JointSLM 0.1

:: DESCRIPTION

The JointSLM R package allows one to simultaneously analyse multiple Depth Of Coverage (DOC) genomic profiles.

::DEVELOPER

the Computational Biology research group in Florence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Windows
  • R package

:: DOWNLOAD

  JointSLM

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 May;39(10):e65. doi: 10.1093/nar/gkr068. Epub 2011 Feb 14.
Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm.
Magi A, Benelli M, Yoon S, Roviello F, Torricelli F.