readbio

pval_computing <- function(tab, output) {
    t <- read.table(tab);
    cat("reading", tab, "Done\n")
    p.val <- rep(NA, times = nrow(t));
    ind_1 <- seq(1:nrow(t));


     #chr1    3101    3200    4       0       68      4       0       53
     #chr       stt     end     #ofSites c_num  t_num   #ofSites        c_num   t_num
     p.val[ind_1] <- lapply(ind_1, function(x) fisher.test(matrix(c(t[x, 5], t[x, 8], t[x, 6], t[x, 9]), nrow = 2))$p.val);

readbio

#!/usr/bin/perl -w
use strict;
##################################################
#This script is to convert tab-delimited file to #
#Exel sheets.                                    #
##################################################
use Excel::Writer::XLSX;

my ($tab, $out) = @ARGV;
die usage() unless @ARGV == 2;

readbio

#!/opt/local/bin/perl -w
use threads;
use strict;
use warnings;

# SOURCE REF: http://chicken.genouest.org/perl/multi-threading-with-perl/

my @a = ();
my @b = ();

readbio

library(DESeq);
data_pnas<-read.table("readCount.res",header=T,row.names=1);

head(data_pnas);

data_pnas_desi<-data.frame(row.names=colnames(data_pnas),condition = c("Sample_g1","Sample_g2","Sample_g3","Sample_g4"),libType  =  c("single-end","single-end","single-end","single-end"));

condition = data_pnas_desi$condition;condition;

cds  =  newCountDataSet(data_pnas,  condition);

readbio

#!/usr/bin/python

import sys
import re

gene_list = sys.argv[1]
motif = sys.argv[2]

#print(gene_list)
#print(motif)

readbio

library(ggplot2)
cc<-read.csv("density_plot.csv",header=T)
diff<-cc[,3]-cc[,2]
p<-ggplot()+geom_density(aes(diff),colour="royalblue", fill="royalblue",alpha=.3)+geom_vline(xintercept=0, linetype="dashed")+xlab("mutant minus WT");ggsave("density_plot.pdf", p)

readbio

library(ggplot2)
cc<-read.csv("density_plot.csv",header=T)
diff<-cc[,3]-cc[,2]
p<-ggplot()+geom_density(aes(diff),colour="royalblue", fill="royalblue",alpha=.3)+geom_vline(xintercept=0, linetype="dashed")+xlab("mutant minus WT");ggsave("density_plot.pdf", p)

readbio

# Note: using the devel versions of both packages!
library(DESeq) # version 1.9.11
library(edgeR) # version 2.99.8
library(VennDiagram)

# Read in data ------------------------------------------------------------

## Use pasilla data
datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )
datafile