Stephen Turner stephenturner

What if a function in a package has no examples? Or is poorly exampled? Wouldn't it be nice to find functioning instances of it "in the wild"?

Via Twitter, Noam Ross taught me a clever way to do such searches on GitHub. Put this into the GitHub search box to see people using the llply() function from plyr:

"llply" user:cran language:R

Or just click here.

Installing gcc 4.8 and Linuxbrew on CentOS 6

The GCC distributed with CentOS 6 is 4.4.7, which is pretty outdated. I'd like to use gcc 4.8+. Also, when trying to install Linuxbrew you run into a dependency loop where Homebrew's gcc depends on zlib, which depends on gcc. Here's how I solved the problem.

Note: Requires sudo privileges.

Resources:

http://superuser.com/a/676337/88393: Forum response on using CERN's open Scientific Linux distribution of RHEL's developer toolset.
http://linux.web.cern.ch/linux/devtoolset/: CERN's developer toolset installation instructions.

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

	## devtools::install_github("stephenturner/msigdf")
	library(msigdf)
	library(dplyr)
	library(clusterProfiler)

	c2 <- msigdf.human %>%
	filter(collection == "c2") %>% select(geneset, entrez) %>% as.data.frame

	data(geneList)
	de <- names(geneList)[1:100]

	# Compile and install htslib, bcftools, samtools 1.9 to home directory

	# Set up dirs where stuff will be installed
	mkdir -p ${HOME}/bin/htslib
	mkdir -p ${HOME}/bin/bcftools
	mkdir -p ${HOME}/bin/samtools

	# Make a dir to build
	mkdir -p ${HOME}/tmp