danielecook

wget 'ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data'
egrep "\t9606\t" homologene.data | sort | cut -f 1,3,4 > human.txt
egrep "\t6239\t" homologene.data | sort | cut -f 1,3,4 > celegans.txt
join -1 1 -2 1 -t $'\t' human.txt celegans.txt | cut -f 2,3,4,5 | sort | echo -e "Human_Entrez\tHuman_Symbol\tElegans_Entrez\tElegans_Symbol\n$(cat -)" > orthologs.txt
rm human.txt celegans.txt homologene.data

msund

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nimishzynga

tell application "System Events"
	-- get current clipboard contents as a string
	set CurrentClipboard to the clipboard as string
	
	-- set the clipboad to your password	
	set the clipboard to "Y0urVPNPa$$w0rd"
	
	-- start playing with the VPN	
	tell current location of network preferences
		

drewconway

# Get StackOverflow data
get.stack<-function(tok) {
    # Must check for XML install, thanks onertipaday!
    if (!require(XML)) install.packages('XML')
    library(XML)
    # Enter a SO tag as character string, and number of tags are returned
    tok<-gsub("(/| )","-",tok)
    tok<-gsub("#","%23",tok,fixed=TRUE)
    base.stack<-"http://stackoverflow.com/questions/tagged/"
    stack.tree<-htmlTreeParse(paste(base.stack,tok,sep=""),useInternalNodes=TRUE)

lindenb

REF=/path/to/ref.fasta
.PHONY:all

all: align/variants.vcf

align/variants.vcf:  align/Sample1_sorted.bam  align/Sample2_sorted.bam  align/Sample3_sorted.bam 
	/path/to/samtools mpileup -uf ${REF}  $^  |\
	/path/to/bcftools view -vcg - >$@

mbq

#AUROC calculation code
auroc<-function(score,cls){
 n1<-sum(!cls); sum(cls)->n2;
 U<-sum(rank(score)[!cls])-n1*(n1+1)/2;
 return(1-U/n1/n2);
}

#... as a cryptic one-liner
auroc1l<-function(score,cls)
 mean(rank(score)[cls]-1:sum(cls))/sum(!cls)

1wheel

d3-jetpack's d3.conventions can now create canvas and html elements. Here d3.conventions({layers: 'csd'}) makes an canvas ctx, svg and div with a shared coordinate system. Yellow shapes are drawn on canvas, cyan on svg and purple on html.

Layers are position absolutely on top of each other in the order listed in the layer string. To create an svg with two canvas elements on top:

var {layers: [svg, bg_ctx, fg_ctx]} = d3.conventions({layers: 'scc'})

Hurricane How-To describes using multiple renders for something more practical than bouncing circles.

johan

Click "raw" below to install. Requires Google Chrome, Firefox + Greasemonkey, or some other browser supporting user scripts / content scripts / user javascript.

msund

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hypercompetent

pearson_residuals <- function(counts, theta = 100) {
  counts_sum0 <- as(matrix(Matrix::colSums(counts),nrow=1),"dgCMatrix")
  counts_sum1 <- as(matrix(Matrix::rowSums(counts),ncol=1),"dgCMatrix")
  counts_sum <- sum(counts@x)
  
  #get residuals
  mu <- (counts_sum1 %*% counts_sum0) / counts_sum
  z <- (counts - mu) / sqrt(mu + mu^2/theta)
  
  #clip to sqrt(n)