Coding Standards for the USC Biostats group
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Software Development Standards

This project's main contents is located in the project's Wiki:

Coding Standards

  1. Coding Standards
  2. Software Thinking
  3. Development Workflow
  4. Misc

We do have some direct guidelines developed as issue templates here.

Bioghost Server

  1. Introduction
  2. Setup
  3. Cheat Sheet

HPC in R

Happy Scientist Semminars

The Happy Scientist Semminars are educational seminars sponsored by Cores C and D of the Biostats Program Project award. This series, the "Happy Scientist" seminar series, is aimed at providing educational material for members of Biostats, both students and faculty, about a variety of tools and methods that might prove useful to them. If you have any suggestions for subjects that you would like to learn about in future, please send email to Paul Marjoram at ( Our agenda will be driven by your specific interests as far as is possible.

  1. Seminar 1: Introduction to Collaborating with GitHub (materials)

  2. R Package Template (materials)

  3. Yet Another 'Writing R packages' tutorial (materials)

  4. A brief introduction to using R for high-performance computing (materials)

  5. The "Happy Scientist" Workshop 1 An introduction to high-performance computing using R (presentation and materials)

USCbiostats R packages

  • aphylo Statistical inference of genetic functions in phylogenetic trees
  • fdrci Permutation-Based FDR Point and Confidence Interval Estimation
  • GxEScanR R version of GxEScan
  • amcmc Adaptive and other Markov Chain Monte Carlo methods
  • rphyloxml Read and write phyloXML files in R
  • partition
  • LUCid Latent and Unknown Cluster Analysis using Integrated Data
  • jsPhyloSVG htmlwidgets for the jsPhyloSVG javascript library
  • MergeBinaryDosage R package for merging binary dosage files
  • polygons
  • BinaryDosage Converts VCF files to a binary format