USCbiostats/Pm566-syllabus-outline

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USCbiostats/Pm566-syllabus-outline

USCbiostats

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Our latest thoughts on what should be covered in a new PM566 course (Intro to Health Data Science)

slurmR

slurmR: A Lightweight Wrapper for Slurm

software-dev

Coding Standards for the USC Biostats group

partition

A fast and flexible framework for data reduction in R

rbootcamp

R boot camp: Scientific Computing

fmcmc

A friendly MCMC framework

PM566

USC's Introduction to Health Data Science

xrnet

R Package for Hierarchical Regularized Regression to Incorporate External Data

hJAM

hJAM is a hierarchical model which unifies the framework of Mendelian Randomization and Transcriptome-wide association studies.

classy

Simple example of C++ Classes and External Pointers with Rcpp

PM520

PM520 Advanced Statistical Computing

Jupyter Notebook

slurmr-workshop

Workshop on HPC with Slurm, R, and the slurmR package

GxEScanR

R version of GxEScan

barry

barry: Your go-to motif accountant

LUCIDus-old

Latent Unknown Clustering with Integrated Data

LUCIDus

the new version of LUCID

aphylo

Statistical inference of genetic functions in phylogenetic trees

jsPhyloSVG

htmlwidgets for the jsPhyloSVG javascript library

r-parallel-benchmark

Using Rcpp with OpenMP (parfor and SIMD)

docker-example

BHRM

An R function for mixtures analysis in environmental epidemiology.

fdrci

Permutation-Based FDR Point and Confidence Interval Estimation

HiLDA

📦 An R package for inferring the mutational exposures difference between groups.

cit

uscrbootcamp

An R package to help install the USC R Bootcamp: Intro to Data Analysis

causnet

Find globally optimal causal network

extendGeneAnnotations

iMutSig

iMutSig: a web application to identify the most similar mutational signature using shiny

Methylation-variability

ENmixUSC

handbook

software-dev-site

figi

All code used in FIGI analyses, plots, documentation, presentations.

LinGxEScanR

laerug-hpc-w-r-nov2018

LAsBEST

Repository of USC's LA's BEST program. https://lasbest.usc.edu/

aws-notes

Random notes on how to use AWS for our research

pruner

pruner: Implementing the Felsenstein's Tree Pruning algorithm

PM570-Colab

Repository for USC PM570 - Statistical Methods in Human Genetics

Jupyter Notebook

research-pipelines

Happy Scientist Seminar: Research Pipelines

bayesnetworks

C++ program to fit Bayesian networks, illustrated with simulated data from P3 of our IMAGE grant application

badges

Badges for USC's Biostats repositories

BinaryDosage

Converts VCF files to a binary format

AnnoQR

R client wrap for AnnoQ API

ACDC

Association of covariance to detect differential co-expression