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# Author : Danny Arends | |
# Purpose : create an MRI table from the format provided by our MRI reader | |
months <- rbind(c("Jan",31),c("Feb",28),c("Mar",31),c("Apr",30),c("May",31),c("Jun",30), | |
c("Jul",31),c("Aug",31),c("Sep",30),c("Oct",31),c("Nov",30),c("Dec",31)) | |
createMRItable <- function(MRIdata, description){ | |
dates <- strsplit(unlist(lapply(strsplit(as.character(MRIdata[,"TimeDateDura"]),";"),"[",1))," ") # Get the malformed dates | |
MRIdata[,"TimeDateDura"] <- unlist(lapply(dates, function(x){ # Transform to DD/MM/YY |
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# | |
# Call expression from aligned SRA reads | |
# copyright (c) 2022 - Danny Arends | |
# | |
library("GenomicAlignments") | |
library("GenomicFeatures") | |
library("Rsamtools") | |
library("preprocessCore") | |
library("vioplot") |
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# Add yourself to the sudo group | |
su - | |
usermod -aG sudo danny | |
exit | |
# Install the virtual box guest additions | |
cd /media/cdrom0 | |
sudo sh ./VBoxLinuxAdditions.run | |
# Install R and deps |
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<!DOCTYPE HTML> | |
<head> | |
<title>DannyArendsTwitchOverlayApp</title> | |
<meta content="text/html;charset=utf-8" http-equiv="Content-Type"> | |
<meta content="utf-8" http-equiv="encoding"> | |
<script src="https://extension-files.twitch.tv/helper/v1/twitch-ext.min.js"></script> | |
<script src="js/secret.js"></script> <!-- Contains startTwitch function which calls getAppToken with Client-ID and Client-Secret --> | |
<script> | |
var audio1 = new Audio('Audio/teleport.mp3'); |
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# | |
# Download the earth texture from: https://www.solarsystemscope.com/textures/, open in MS Paint, scaled down to 50% size and save as BMP | |
# Or download it from: https://www.dannyarends.nl/etc/img/2k_earth_daymap.bmp | |
# JHU CovID19 data from: CSSE at Johns Hopkins University (CSSEGISandData) | |
# copyright GPL-3 by Danny Arends - Molekulare Zuchtungsbiology - HU Berlin | |
# Written May, 2020, last modified May, 2020 | |
# | |
# Change: /path/to/ and set the working dir to the BMP image | |
setwd("/<path>/<to>/") |
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<!DOCTYPE html> | |
<html> | |
<head> | |
<meta charset="UTF-8"> | |
<script type="javascript" src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.6/d3.min.js"></script> | |
</head> | |
<body> | |
Open the developer console in firefox to see the error | |
</body> | |
</html> |
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# Bioconductor packages | |
source("http://bioconductor.org/biocLite.R") | |
biocLite(ask=FALSE) | |
biocLite(c("preprocessCore", "biomaRt", "affy", "limma", "beadarray", "ggplot2", "impute", "DESeq2", "Rsamtools", "vsn")) | |
biocLite(c("topGO", "GO.db", "KEGG.db", "MotifDb", "seqLogo", "motifStack")) | |
biocLite(c("Biostrings", "GenomicAlignments", "GenomicFeatures", "BiocParallel")) | |
biocLite(c("BSgenome.Mmusculus.UCSC.mm10", "TxDb.Mmusculus.UCSC.mm10.ensGene")) | |
biocLite(c("gcrma", "lumi", "ShortRead", "cdfpackage", "seqinr", "reshape2", "plyr", "scales")) | |
# CRAN packages |
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phi <- 0 | |
while(TRUE){ | |
plot(sin(phi + 1:20), col=c("black","black","red"), cex=3, pch=c("☢","☠","♥")) | |
Sys.sleep(0.1) | |
phi = phi +0.3 | |
} |
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library("qtl") # Load the library | |
data(multitrait) # Load the data | |
multitrait # Show the library | |
pull.pheno(multitrait, pheno.col = 1) # Shows the phenotype values of phenotype 1 | |
hist(pull.pheno(multitrait, pheno.col = 1)) # Create a histogram | |
# Plot a map versus the other ones | |
plot.map(multitrait, est.map(multitrait)) |
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*~ | |
*.rdf | |
*.n3 |
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