G-NEST – Gene Neighborhood Scoring tool

G-NEST

:: DESCRIPTION

G-NEST combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

G-NEST

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 28;13:253. doi: 10.1186/1471-2105-13-253.
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.
Lemay DG1, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS.

NBC 1.0 – Neighborhood Breakpoint Conservation

NBC 1.0

:: DESCRIPTION

NBC (Neighborhood Breakpoint Conservation) is a method that identifies recurrent copy number variants in multiple individuals using Array Comparative Genomic Hybridization (aCGH).aCGH computes the ratio of test:reference DNA for probes located on the reference genome. NBC first uses a Bayesian changepoint algorithm to identify probes, called breakpoints, that change from low-to-high or high-to-low copy number with high probability. A binomial statistic is then applied to identify breakpoints and pairs of breakpoints that appear in a statistically significant number of individuals.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsx/WIndows
Java

:: DOWNLOAD

NBC

:: MORE INFORMATION

Citation

A. Ritz, P.L. Paris, M.M. Ittmann, C. Collins, and B.J. Raphael. (2011)
Detection of Recurrent Rearrangement Breakpoints from Copy Number Data.
BMC Bioinformatics 2011, 12:114 doi:10.1186/1471-2105-12-114

NEMO v0.1 – Neighborhood based multi-omics Clustering

NEMO v0.1

:: DESCRIPTION

NEMO is a multi-omic clustering algorithm. NEMO supports data in which some omics were measured for only a subset of the samples.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/ MacOsX
R
SNFtool

:: DOWNLOAD

NEMO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Sep 15;35(18):3348-3356. doi: 10.1093/bioinformatics/btz058.
NEMO: cancer subtyping by integration of partial multi-omic data.
Rappoport N, Shamir R.

AsVis 20051125 – Visualizing Association Rules in SNP Neighborhoods

AsVis 20051125

:: DESCRIPTION

AsVis is a web application for visualizing association rules obtained from short, sequential data (such as SNP neighborhoods) by means of data mining. It allows the association rules to be sorted by a variety of measures and filtered by position, enabling fast, interactive data exploration.

::DEVELOPER

Group of Data mining in genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Web Server
CGI

:: DOWNLOAD

AsVis

:: MORE INFORMATION

Citation

Kimmo Kulovesi et al
Visualisation of Associations Between Nucleotides in SNP Neighbourhoods
Workshop on Intelligent Data Analysis in bioMedicine and Pharmacology (IDAMAP’06), Verona, Italy, August 2006.