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Bioinformatics Software

Statistical Tools

Software Name

Developer

Description

PCPD

George Nelson

PCPD is an application of principal component analysis to transform multiple clinical outcome statistics to independent statistics, and to assign an overall statistical significance.

Ferret
Ferret GUI

George Nelson
Carl McIntosh

User-friendly EM-based haplotype inference tool, with ability to scan for haplotype blocks across a region.

gmodels

Randall Johnson

Various R programming tools for model testing (part of gregmisc package).

hwde

Randall Johnson

Models and tests for departure from Hardy-Weinberg equilibrium and independence between loci.

Data Management, Data Mining and Genome Tools

Software Name

Developer

Description

ARGANALYSIS

Jim Lautenberger

Computational module: Performs categorical and Cox model analyses

ARGARRAY

James Lautenberger

Array of rectangles, color indicates significance or strength of association

ARGHIGHWAY

James Lautenberger

User surveys 3D plot; height of bars represents significance, and color represents strength and direction, of association

ARGTRAX

James Lautenberger

Graphic display of strength and significance of statistics, bar graphs, KM plots

CocoaGWASNetCDF

Carl McIntosh

Massive SNP data storage, management and Quality Control Software

FERRETSophie LimouUser-friendly tool to quickly extract data from the 1000 Genomes Project. Outputs are suitable for PLINK and HaploView.

File Converter
(MAC or WIN)

Bailey Kessing

Converts file formats between various file formats

GARField

Joan Pontias

Genome Annotation Resource Field Felis catus v12.2

HapMap Express (beta)

Randall Johnson

 

kmplot

George Nelson

4 Kaplan-Meier plots, annotated with Cox model statistics

Manhattan Plot

Randall Johnson

generation of Manhattan plots of genome-wide association data 

QC Checker

Carl McIntosh
Jennifer Troyer

GWAS Production Quality Control Software

SNP Edit

Carl McIntosh
Jennifer Troyer

Massive SNP data storage, management and Quality Control Software

SNP Trawler
(MAC or WIN)

Bailey Kessing

Searches NCBI databases for SNP and gene information

Tagger Companion
(MAC or WIN)

Bailey Kessing

Collates all of Tagger's results files into readable and usable file formats