Software for QTL Data Analysis

QTL Analysis

• R/qtl: basic & advanced QTL tools
• R/qtlbim: Bayesian Interval Mapping for Multiple QTLs
• R/qtlhot: QTL Hotspots and Causal Architecture
• R/qtlnet: Causal Inference of QTL Networks
• R/qtlyeast: QTL Analysis of Brem & Kruglyak Yeast Data (GITHUB source or Windows ready version)

• QTL Cartographer (Windows menu-driven stand-alone)

Gene Expression Microarray Software

• Gary Churchill's Statistical Genetics Group, Jackson Labs
• GeneX Analysis Tools, NCGR and UC Irvine
• Tony Long's Statistical Analysis and Molecular Biology Tools, UC Irvine
• Leif Peterson's Genetic Epidemiology (GenEpi), Baylor College of Medicine
• Terry Speed's Software Page, UC Berkeley
• Rob Tibshirani's Significance Analysis of Microarrays (SAM), Stanford U
• Wing Wong's dChip (Li Wong 2000 PNAS), Harvard U

• Gene Expression Data Analysis (GEDA), UW-Madison Biostatistics & Medical Informatics Department
  • GEDA's R System Software for Microarray Data Analysis
  • GEDA Related Sites (includes software links)
• Stanford Microarray Database (SMD)
• NIH/NHGRI Microarray Project

R System Software for Microarrray Data Analysis

• R Project (documentation, system download)
• Information on R and related systems (S and Splus)

• GeneSOM Self-Organizing Maps (J Yan 2001)
• microarray.zip (routines for analysis used in Newton et al. (2000) and in Lin et al. (2001))
• sma (Terry Speed's group)