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library(ggplot2)
library(tidyverse)
library(readr)
sra_stat <- read_csv("https://www.ncbi.nlm.nih.gov/Traces/sra/sra_stat.cgi")
sra_stat$date <- as.Date(sra_stat$date, format = "%m/%d/%Y")

ggplot(sra_stat, aes(x = date, group = 1)) +
  geom_area(aes(y = bases / 10^15), fill = "orange", alpha = 0.8) + 
  geom_area(aes(y = bytes / 10^15), fill = "blue", alpha = 0.8) + 
  labs(title = "Amount of Sequencing Data in SRA", 

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#!/bin/bash
#convert all gddoc documents to pdf
#needs jq: https://stedolan.github.io/jq/download/
shopt -s nullglob
for g in *.gddoc
do
	url=$(jq -c '.url' $g)
	url="${url%/edit?usp=drivesdk\"}"
	url="${url#\"}"

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library(foreach)
library(stringr)
library(biomaRt)

read_gmt <- function(gmt_file){
  
  conn <- file(gmt_file,open="r")
  all_lines <-readLines(conn)
  result <- foreach(line = str_split(all_lines, "\t"), .combine = bind_rows) %do% {
    data_frame(id = line[1], gene_id = line[-c(1,2)])

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#obtained from ftp://ftp.ensembl.org/pub/grch37/release-87/regulation/homo_sapiens/homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117.gff.gz
#date: 12/01/2017
library(stringr)
library(tidyr)

homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117 <- read.delim("/local/home/mlist/Projects/homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117.gff", header=FALSE)

ensembl_reg_hg19 <- tidyr::separate(homo_sapiens.GRCh37.Regulatory_Build.regulatory_features.20161117, col = V9, into = c("ID", "bound_end", "bound_start", "description", "feature_type"), sep = ";")
apply(ensembl_reg_hg19, 2, function(x) str_replace_all(x, pattern = ".*=", ""))
ensembl_reg_hg19_tidy <- apply(ensembl_reg_hg19, 2, function(x) str_replace_all(x, pattern = ".*=", ""))

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# Load dependencies
# install DeepBlueR from bioconductor 
# http://bioconductor.org/packages/release/bioc/html/DeepBlueR.html
library(DeepBlueR)
library(dplyr)
library(tidyr)

# List all BLUEPRINT samples
blueprint_samples <- deepblue_list_samples(
    extra_metadata = list("source" = "BLUEPRINT Epigenome"))

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# authentication, register for DeepBlue, log in, open your account info,
# copy and paste user key here
auth_key <- "xxxxxxxxxx"

#dependencies
library(foreach)
library(matrixStats)
library(DeepBlueR)
library(stringr)
library(corrplot)

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### PLAIN INSTALLATION ###

#Download the installer for Microsoft R Open built for Ubuntu 15
wget https://mran.revolutionanalytics.com/install/mro/3.2.3/MRO-3.2.3-Ubuntu-15.4.x86_64.deb

#Install package ignoring the missing libjpeg dependency
sudo dpkg -i --ignore-depends libjpeg8 MRO-3.2.3-Ubuntu-15.4.x86_64.deb 

#At this point you can already use MRO but plotting won't work! 

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  setAs("RnBeadSet", "RnBeadRawSet", function(from){ 
    new(Class = RnBeadSet,
        pval.sites = from@pval.sites,
        pval.regions = from@pval.regions,
        qc = from@qc,
        pheno = from@pheno,
        sites = from@sites,
        meth.sites = from@meth.sites,
        covg.sites = from@covg.sites,
        regions = from@regions,

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sudo docker images -a | awk 'NR >= 2 {printf "%s ",$3}' | xargs sudo docker rmi -f

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### R functions to consume the KeyPathwayMinerWeb RESTful API ###
### Authors: Markus List and Martin Dissing-Hansen ###

# Package dependencies. Make sure those are installed
library(RCurl)
library(rjson)
library(foreach)

# Helper method for base64 encoding. Needed to transfer network and dataset files #
base64EncFile <- function(fileName){