jenzopr

#!/usr/bin/env python
__author__ = 'Jens Preussner'
__license__ = 'MIT'

import argparse
import logging
import sys

if __name__ == "__main__":
    #

jenzopr

library(zoo)
calc_dm = function(expr, func=median) {
  if( is.null(rownames(expr)) ) { rownames(expr) = 1:nrow(expr) }
  
  # Calculate log10 mean of the rows
  m = log10(rowMeans(expr))
  names(m) = rownames(expr)
  
  # Calculate the squared cv
  cv2 = apply(expr, 1, function(x) { (sd(x)/mean(x))^2 })

jenzopr

##gff-version 3
chr3	doi:10.1186/1471-2164-12-152	enhancer	34761079	34762078	1	+	.	is_validated=false;nearest_gene=Sox2;distance=108618;location=intergenic
chr7	doi:10.1186/1471-2164-12-152	enhancer	3206000	3206999	1	+	.	is_validated=false;nearest_gene=mmu-mir-290;distance=11627;location=intergenic
chr8	doi:10.1186/1471-2164-12-152	enhancer	89003102	89004101	1	+	.	is_validated=true;nearest_gene=Sall1;distance=23147;location=intergenic
chr9	doi:10.1186/1471-2164-12-152	enhancer	110947497	110948496	1	+	.	is_validated=false;nearest_gene=Tdgf1;distance=1430;location=upstream
chr12	doi:10.1186/1471-2164-12-152	enhancer	86501051	86502050	0,9999	+	.	is_validated=false;nearest_gene=Esrrb;distance=19570;location=genic
chr4	doi:10.1186/1471-2164-12-152	enhancer	55475129	55476128	0,9999	+	.	is_validated=false;nearest_gene=SNORA17;distance=5970;location=upstream
chr8	doi:10.1186/1471-2164-12-152	enhancer	43320647	43321646	0,9999	+	.	is_validated=false;nearest_gene=Zfp42;distance=13711;location=intergenic
chr9	doi:10.1186

jenzopr

{
"collection" : {
	"version" : "1.0",
	"href" : "http://example.com/collection",
	"links" : [
		{"rel" : "profile", "href" : "https://gist.github.com/jenzopr/3fb7b358be060711c7da#file-profile-xml"},
	],
	"items" : [],
	"queries" : [
		{

jenzopr

#
# This is an example YAML profile for cassandra-stress
#
# insert data
# cassandra-stress user profile=/home/jake/stress1.yaml ops(insert=1)
#
# read, using query simple1:
# cassandra-stress profile=/home/jake/stress1.yaml ops(simple1=1)
#
# mixed workload (90/10)