ExomeCopy 1.32.0 – Copy Number Variant Detection from Exome Sequencing Read Depth

ExomeCopy 1.32.0

:: DESCRIPTION

ExomeCopy implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

::DEVELOPER

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ExomeCopy

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1).
Modeling read counts for CNV detection in exome sequencing data.
Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.

CNVnator 0.3 – CNV Discovery and Genotyping from Depth of Read Mapping

CNVnator 0.3

:: DESCRIPTION

CNVnator is a tool for Copy number variation (CNV) discovery and genotyping from depth of read mapping.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CNVnator

:: MORE INFORMATION

Citation:

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Abyzov A, Urban AE, Snyder M, Gerstein M.
Genome Res. 2011 Jun;21(6):974-84. Epub 2011 Feb 7.

CODOC 0.0.2 – Analysis and Compression of Depth of Coverage Signals

CODOC 0.0.2

:: DESCRIPTION

CODOC is a compressed data format and API for coverage data stemming from sequencing experiments

::DEVELOPER

Niko Popitsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 CODOC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 28. pii: btu362. [Epub ahead of print]
CODOC: Efficient Access, Analysis and Compression of Depth of Coverage Signals.
Popitsch N.

DEPTH 2.8.7 – Measure Extent of Atom/Residue Burial within Protein

DEPTH 2.8.7

:: DESCRIPTION

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein–protein interaction hot spots, post-translational modification sites and sequence variability.

::DEVELOPER

Bioinformatics Institute of Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 DEPTH

:: MORE INFORMATION

Citation:

Kuan Pern Tan; Raghavan Varadarajan; M. S. Madhusudhan
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr356

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.