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Itoshi NIKAIDO dritoshi

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dritoshi / file0.txt
Last active June 16, 2016 11:54
Bayes LinuxのGalaxyでRNA-seq解析を行う ref: http://qiita.com/dritoshi/items/c0272ae6c1548210ab99
curl -ssL https://q-brain2.riken.jp/bayes/vm/dl.sh | bash -s
@dritoshi
dritoshi / file0.txt
Last active August 30, 2017 15:37
Bayes Linuxを完成した仮想マシンイメージから起動する ref: http://qiita.com/dritoshi/items/1d95480022feb25cb5ac
curl -O https://q-brain2.riken.jp/bayes/vm/bayesvm_1.4.0.ova # ovaをダウンロード
curl -O https://q-brain2.riken.jp/bayes/vm/bayesvm_1.4.0.ova.md5 # md5をダウンロード
md5sum -c bayesvm_1.4.0.ova.md5 # ファイルをチェック
@dritoshi
dritoshi / file0.txt
Last active March 31, 2017 08:31
Bayes Linuxでバイオインフォマティクス解析環境を簡単に再現良く構築する ref: http://qiita.com/dritoshi/items/707d3dd1fe9ed4f3b5b6
$ git clone https://github.com/BioDevOps/basicsetup
@dritoshi
dritoshi / gist:ab9c2bc36156cf090228
Created August 26, 2014 04:24
Karabiner private.xml for RStudio
<?xml version="1.0"?>
<root>
<appdef>
<appname>RSTUDIO</appname>
<equal>org.rstudio.RStudio</equal>
</appdef>
<item>
<name>RSTUDIO</name>
<list>
<item>
@dritoshi
dritoshi / gist:9204605
Created February 25, 2014 07:46
Calculate melting temperature (Tm)
source("http://bioconductor.org/biocLite.R")
biocLite("HELP")
library("HELP")
calcTm("ATGCATGC")
@dritoshi
dritoshi / gist:8516258
Created January 20, 2014 07:20
R から iOS にお知らせ。notifyR package と pushover を利用する。
library("notifyR")
userkey <- "XXXXXXXXXXXXXXXXXXX"
send_push(userkey,
title = "Hello from R!",
message = "Rからこんにちは!"
)
@dritoshi
dritoshi / gist:7113447
Created October 23, 2013 06:26
OS X Mavericks (10.9) を入れたら homebrew が動かなくなったので reinstall した
rm -rf /usr/local/Cellar /usr/local/.git && brew cleanup
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
brew prune
brew doctor
@dritoshi
dritoshi / ensmust2eg.r
Created October 5, 2012 04:36
Convert EnsEMBL Gene ID to NCBI Entrez Gene ID in R
library("org.Mm.eg.db")
my.ensmusg <- c("ENSMUSG00000000275", "ENSMUSG00000002844", "ENSMUSG00000003868", "ENSMUSG00000091821", "HOGE")
a <- sapply(my.ensmusg, function(x) exists(x, org.Mm.egENSEMBL2EG))
my.ensmusg.existed <- my.ensmusg[a]
my.ensmusg.existed
@dritoshi
dritoshi / gene_symbol2locus.rb
Created July 10, 2012 05:32
Transforming gene symbol to genomic position
#!/usr/bin/env ruby
require "rubygems"
require "biomart"
require "pp"
htgt = Biomart::Server.new( "http://www.sanger.ac.uk/htgt/biomart" )
ensmus = htgt.datasets["mmusculus_gene_ensembl"]
# pp ensmus.list_filters
@dritoshi
dritoshi / mixpoissfit.m
Created May 2, 2012 15:12
Mixture Poisson parameter estimates
clf('reset');
% Definition of pdf
pdf_mixpoiss = @(x, p, lambda1, lambda2) p * poisspdf(x, lambda1) ...
+ (1 - p) * poisspdf(x, lambda2);
% Make a demo data
rng(218, 'twister');
p = 0.4;
n = 10000;