Affymetrix Snp

SNP Analyser was developed as an easy-to-use and useful utility for the efficient analysis and management of Affymetrix SNP DMET Data analysis. SNP Analyser is a software that was designed with the help of the Java programming language. Platforms: Windows

Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker. For information on accessing B Allele Frequencies for Illumina data, Platforms: Mac

Device::SNP is a Perl extension for the GE Fanuc SNP-X serial protocol as used by GE Fanuc DataPanel data terminals. See http://www.gefanuc.com/en/ProductServices/VisPCSolutions/DataPanel/index.html SYNOPSIS use Device::SNP; my $s = new Device::SNP::Slave( Portname => /dev/ttyUSB0, Debug... Platforms: *nix

Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files. SYNOPSIS use Bio::Affymetrix::CDF; # Parse the CDF file my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0}); $cdf->parse_from_file("foo.cdf"); # Find some fun facts about this chip type print... Platforms: *nix

This script imports Affymetrix DMET data. Hemizygous markers are converted to homozygous markers, and tri-allelic markers are converted into two columns, each containing the major allele and one of the minor alleles. A DMET marker map (see below) can be selected after selecting the DMET report... Platforms: Mac

The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis Platforms: Windows, Mac, Linux

We attempt to reproduce and efficiently implement in MATLAB publicly available methods of Affymetrix MAS 5 and GCOS 1.2 software that perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files and create corresponding CHP data structures:1. CHP data structure is... Platforms: Matlab

This user interface allows a user to load some Affymetrix data in an Excel file and perform some basic operations on it - log transform, log ratio, normalization, noise reduction, filtering, PCA and clustering, in addition to some visualizations like profile plots, boxplots and matrix... Platforms: Matlab

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data. Platforms: *nix

AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data. Platforms: Mac, BSD, Linux

Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies. Platforms: Windows, Mac, Linux

MAGMA: Multiobjective Analyzer for Genetic Marker AcquisitionA genetic algorithm for generating SNP tiling paths from a large SNP databasebased on the competing objectives of cost (number of SNPs) and coverage (haplotype blocks):Hubley R., Zitzler Platforms: Windows, Mac, Linux

GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description... Platforms: Matlab

This script creates a binary spreadsheet to indicate if there exists a rare variant in the window centered about the current marker. At chromosome edges, the maximum number of markers up to the window size is used without running into the next chromosome. Platforms: Mac

Avenzoar is a one-year exploration of renal cell carcinoma morphology and its related single nucleotide polymorphisms (SNPa) as a method of automating diagnosis of cancer by using a computer-aided decision tree controlled by analytical statistics. Features Detects and comes to a... Platforms: *nix

libspectrum is a library designed to make the input and output of some ZX Spectrum emulator files slightly easier. libspectrum is intended to be usable on Unix variants, Mac OS X and Win32. Currently, it is mainly (only?) used by Fuse, but other Spectrum emulator and utility authors are... Platforms: *nix

PGDSpider was built using the Java programming language as a conversion app for population genetics and genomics programs. The software facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic... Platforms: Windows

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence... Platforms: Windows

GNomEx is Genomic LIMS and Analysis Project Center designed by the Huntsman Cancer Institute for use by microarray and next generation sequencing core facilities and large research laboratories. KWs: Illumina, Affymetrix, Agilent, MAGE, MySQL/Flex... Platforms: Windows

The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina GAIIx and the Roche GS yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing platforms... Platforms: Windows