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2014-12-08-combine-r-code

Scripts, data, and exercise solutions from the live coding portion of the 2014-12-08-combine-r Software Carpentry bootcamp

bad-boyz-cluster

bc

Template for Software Carpentry bootcamp site repository.

bigmemory-rcpp-test

A minimal package for working with bigmemory in Rcpp

bigparallelr

Parallel tools in R

bioinformatics-conference-bingo

Modified for bioinformatics in an Australian context

bootstrapqtl

Bootstrap cis-QTL method that corrects for The Winner's Curse

cardiometabolic_prs_plasma_proteome

Source code and software list for the study "Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases" on bioRxiv (doi: 10.1101/2019.12.14.876474)

data.table

R's data.table package extends data.frame:

dockerfile-dit4c-container-rstudio

git-novice

Software Carpentry introduction to Git for novices.

githubioswitch

A javascript bookmarklet for switching between a Github repository and its Github Pages site

imputegp

R package to impute GlycA glycoproteins from serum NMR data in population studies

lesson-template

Template for remixable lessons.

liftoverplink

A wrapper for liftOver for converting plink genotype data between different genome reference builds

netrep

R package containing functions for assessing the replication/preservation of network topology for weighted gene coexpression network modules in one or more independent datasets through permutation testing.

networktools

An R package containing a collection of tools for working with and visualising large networks.

parprogressbar

Utilities for creating a progress bar that renders in when running in parallel.

plinktools

Miscellaneous functions for supplementing the command line tool plink.

predixcan

PrediXcan Project

python-novice-inflammation

Software Carpentry introduction to Python for novices using inflammation data.

qqman

R code for creating Manhattan plots and Q-Q plots for GWAS

r-alpha-bootcamp-unimelb-notes

r-bootcamp-alpha

Website for the R alpha bootcamp to be run on 2014-09-23 at the University of Melbourne.

r-novice-gapminder

Introduction to R for non-programmers using gapminder data.

rcpp-gallery

Source code for the Rcpp Gallery website

rezbaz-bootcamps

Teaching materials used by the Research Bazaar

rfast

A collection of Rfast functions for data analysis. Note 1: The vast majority of the functions accept matrices only, not data.frames. Note 2: Do not have matrices or vectors with have missing data (i.e NAs). We do no check about them and C++ internally transforms them into zeros (0), so you may get wrong results. Note 3: In general, make sure you give the correct input, in order to get the correct output. We do no checks and this is one of the many reasons we are fast.

shell-novice

Software Carpentry introduction to the shell for novices.

splitstackshape

R functions to split concatenated data, conveniently stack columns of data.frames, and conveniently reshape data.frames.