stephenturner

# 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

ilevantis

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.

stephenturner

## 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]

stephenturner

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The GCC distributed with CentOS 6 is 4.4.7, which is pretty outdated.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.

jennybc

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.

vsbuffalo

# A quick function to save a PBM (http://en.wikipedia.org/wiki/Netpbm_format)
# visualize *a lot* of missing data pretty quickly (outside of R).

writeMissingPBM <- function(x, file) {
  dims <- dim(x)
  x[] <- as.integer(is.na(x))
  con <- file(file, open="wt")
  writeLines(sprintf("P1\n%d %d", ncol(x), nrow(x)), con)
  write.table(x, file=con, sep=" ", col.names=FALSE, row.names=FALSE, quote=FALSE)
  close(con)

seandavi

Usage

To use these scripts:

• Clone this repository: git clone https://gist.github.com/95a4b2ab3b90f6f0bfd9.git snpEffScript
• cd snpEffScript
• make appropriate changes to setup.sh
• call snpEff.sh like so:

arq5x

export SAMPLES="2484-AJ-0001 2484-AJ-0002 2484-AJ-0003"

######################################
# Make FASTQ
######################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
export STEPNAME=ovc-fastq
for sample in `echo $SAMPLES`
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M arq5x@virginia.edu";

arunsrinivasan

require(reshape2)

# data.table commit (1048)
require(data.table)
# Loading required package: data.table
# data.table 1.8.11  For help type: help("data.table")

set.seed(1)
N <- 2e7 # size of DT

seandavi

idat2lumibatch <- function(filenames) {
  # filenames is a character vector of iDAT filenames
  require(illuminaio)
  require(lumi)
  idatlist = lapply(filenames,readIDAT)
  exprs = sapply(idatlist,function(x) {
    return(x$Quants$MeanBinData)})
  se.exprs = sapply(idatlist,function(x) {
    return(x$Quants$DevBinData/sqrt(x$Quants$NumGoodBeadsBinData))})
  beadNum = sapply(idatlist,function(x) {