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http://wavi.bioinfo.cnio.es/

A versatile web-server application for the analysis and visualization of array-CGH data.

Proper citation: waviCGH (RRID:SCR_006662) Copy   

•   Source: SciCrunch Registry

http://probeexplorer.cicancer.org/principal.php

Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool

Proper citation: ProbeExplorer (RRID:SCR_007116) Copy   

•   Source: SciCrunch Registry

http://baygenomics.ucsf.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The BayGenomics gene-trap resource provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. The major goal of BayGenomics is to identify genes relevant to cardiovascular and pulmonary disease.

Proper citation: BayGenomics (RRID:SCR_008168) Copy   

•   Source: SciCrunch Registry

http://cello.life.nctu.edu.tw/

A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment.

Proper citation: CELLO (RRID:SCR_011968) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/fdudbridge/software/pelican

Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.

Proper citation: PELICAN (RRID:SCR_001695) Copy   

•   Source: SciCrunch Registry

http://iomics.us/

A genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods.

Proper citation: iOMICS (RRID:SCR_000239) Copy   

•   Source: SciCrunch Registry

https://github.com/wtsi-npg/Illuminus

A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology.

Proper citation: ILLUMINUS (RRID:SCR_000388) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ldb;

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application that integrate genetic linkage map and physical map (entry from Genetic Analysis Software)

Proper citation: LDB/LDB+ (RRID:SCR_000839) Copy   

•   Source: SciCrunch Registry

http://research.calit2.net/hap/

Software application (entry from Genetic Analysis Software)

Proper citation: HAP 1 (RRID:SCR_000837) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LAMBDAA (RRID:SCR_001128) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LDMET (RRID:SCR_001127) Copy   

•   Source: SciCrunch Registry

http://www.biostat.harvard.edu/complab/dchip/snp.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: DCHIP LINKAGE (RRID:SCR_000835) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/floss/floss.htm

Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software)

Proper citation: FLOSS (RRID:SCR_000836) Copy   

•   Source: SciCrunch Registry

http://null

Software application for calculating the heterozygosity, PIC, and LIC values for polymorphic markers (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: POLYMORPHISM (RRID:SCR_000828) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/EDAC.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: EDAC (RRID:SCR_000829) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/2LD.md

Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.

Proper citation: 2LD (RRID:SCR_000826) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/SQTL/

Software application (entry from Genetic Analysis Software)

Proper citation: SQTL (RRID:SCR_000827) Copy   

•   Source: SciCrunch Registry

https://hsph.harvard.edu/research/price-lab/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: EIGENSOFT/EIGENSTRAT (RRID:SCR_001357) Copy   

•   Source: SciCrunch Registry

http://solar-eclipse-genetics.org

A flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis. (entry from Genetic Analysis Software)

Proper citation: SOLAR (RRID:SCR_000850) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~gqian/software.htm (not available)

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: MRH (RRID:SCR_000841) Copy   

•   Source: SciCrunch Registry