Welcome to BARU software

On this site, we publish software developed in BARU — Biodemography of Aging Research Unit.

See main BARU website for details regarding our organization.

Table of contents

• Temporary pages
  • Software Build System
    • Overview
    • Directory Structure
    • Installation and Preparation
      • Installation and Preparation — System Side
      • Installation and Preparation — User Side
    • Using Installed Software — User’s Perspective
    • Installing a New Package
      • Overview
      • Installation Scripts
        • download-files
        • build
        • install-binaries
        • install-wrappers
        • set-current-version
        • uninstall-binaries
        • uninstall-wrappers
        • filelist-version
      • RR and RRlib
  • Non-R packages (need to find appropriate place)
  • Various testing
    • CodeBlock Testing
    • Shortcode Testing
    • Toy Example
• General Notes
• AGAPS
  • Description
  • Download
  • AGAPS Tutorials
    • Pipeline Tutorial
    • Mediation Tutorial
• MXP — Modular eXpandable framework for building Pipelines
  • MXP Base
    • MXP Documentation
      • MXP Overview and Concepts
      • MXP Installation
      • Syntax of MXP Makefile
      • Running MXP: Command Line
      • How MXP Detects What Targets Should Be Rebuilt
      • Standard MXP Methods
      • Writing Your Method and Parameter Scripts
      • How MXP Finds Scripts to Obtain Target
      • Chaining Pipelines: Using Existing Pipeline in a New One
      • Publishing Pipelines That Can Be Reused by Other Researchers
      • Using Power of Bash Scripting
      • Comparison with Other Frameworks for Building Pipelines
    • Download MXP
    • MXP Change Log
    • MXP Tutorials
      • MXP: Toy Example
  • MXP GWAS: Pipeline for GWAS Analysis
    • MXP GWAS Documentation
      • MXP GWAS Makefile Overview
      • MXP GWAS Methods
        • Method idata
    • Download MXP GWAS
    • MXP GWAS Change Log
• R Packages
  • coxmeg: Cox Mixed-Effects Model for Genome-Wide Association Studies
  • di: Utilities to Calculate Deficit Index (DI)
  • haploR: An R-package for Querying Web-Based Annotation Tools
  • rqt: Utilities for Gene-Level Meta-Analysis
  • stpm: An R Package for Stochastic Process Model
• Miscellanies
  • Challenges
    • SNP Names in dbGaP
• Other Software
  • cophesim: A Comprehensive Simulator of Phenotype-Genotype Connections for Testing Methods of Genetic Analysis
• All Downloads