zhoujj2013

setwd('WGCNA/')
# 	56 breast cancer cell lines were profiled to identify patterns of gene expression associated with subtype and response to therapeutic compounds.
if(F){
  ## https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48213
  #wget -c ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48213/suppl/GSE48213_RAW.tar
  #tar -xf GSE48213_RAW.tar
  #gzip -d *.gz
  ## 首先在GSE48213_RAW目录里面生成tmp.txt文件，使用shell脚本
  # awk '{print FILENAME"\t"$0}' * |grep -v EnsEMBL_Gene_ID >tmp.txt
  ## 然后把tmp.txt导入R语言里面用reshape2处理即可

zhoujj2013

args <- commandArgs(TRUE)
prefix = args[1]

#print(args[c(2:length(args))])

pdf(paste(prefix,".density.pdf",sep=""))
color = rainbow(length(args) - 1)

for (i in 2:length(args)){
    dat = read.table(args[i],header=F)

zhoujj2013

args <- commandArgs(TRUE)
dat =  read.table(file=args[1])

library(ROCR)

predictions = dat$V2
labels = dat$V3

# perform prediction
pred <- prediction(predictions, labels)

zhoujj2013

Plekhg2             10.63065            1
Plekhg3             6.576155            1
Plekhg1             4.555775            1
Plekhg6             0.9426185           1
4930592I03Rik       0.02947105          1
Plekhg4             0.7554405           1
Plekhg5             25.47185            1
Nsa2                38.0276             1
Nampt               27.66735            1
Ndc1                24.23355            1

zhoujj2013

#!/usr/bin/perl -w 

use strict;
use Data::Dumper;
use Getopt::Long;

# Written by [email protected]
# convert sam to wig format

my ($bin,$mq,$normalize, $chunk_size);

zhoujj2013

#!/usr/bin/perl -w

use strict;
use Data::Dumper;

## Written by [email protected]
# import gff3 file to jbrowser by chr
# default jbrowser installation diretory is /var/www/jbrowser/

my ($gff3_f,$outdir) = @ARGV;

zhoujj2013

#/usr/bin/perl -w

use strict;
use Data::Dumper;

## Written by [email protected]
## convert ensembl gtf to gff3 format, just for JBrowser

my ($gtf_f, $chr_list_f) = @ARGV; # ensembl gtf file, gtf from different source are different.

zhoujj2013

#!/usr/bin/perl -w

use strict;

my $f = shift; # input fasta file download from batch Entrez (http://www.ncbi.nlm.nih.gov/sites/batchentrez)
open IN,"$f" || die $!;
$/ = ">"; <IN>; $/ = "\n";
while(<IN>){
	chomp;
	my $id = $_;

zhoujj2013

#!/usr/bin/perl -w

use strict;
use Data::Dumper;

my ($file, $max_gap, $min_block) = @ARGV;

my %fa;
my @id;

zhoujj2013

# install debian linux from official website (with web server, ssh server application)
# source.lst for different district:

# update the source.lst and then update debian linux
su root
# input the password
cp new_source.lst /etc/apt/source.lst
apt-get update

# or edit by vi /etc/apt/source.lst, then update