davetang

#I want to fetch sequences from
#my_random_loci and my_refseq_tss
head(my_random_loci,2)
    chr    start      end strand
1 chr18 59415403 59415407      +
2 chr22  8535632  8535636      -

#install if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome.Hsapiens.UCSC.hg19")

davetang

#install if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")

#load library
library(GenomicRanges)

#create a GRanges object given an object, my_refseq_loci
head(my_refseq_loci,2)
#   refseq_mrna chromosome_name transcript_start transcript_end strand

davetang

#install if necessary
install.packages("randomForest")

#load library
library(randomForest)

#I have two sets of dinucleotide counts stored in
#my_random_loci_seq_di and my_refseq_tss_seq_di

head(my_refseq_tss_seq_di,2)

davetang

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <matrix.dat>\n";
my $infile = shift or die $usage;

my $accession = '';
my $start = 0;

davetang

#!/usr/bin/env perl

use strict;
use warnings;

=head1 NAME

This scripts converts a psl file into a bed file written by Dave Tang.

=head1 SYNOPSIS

davetang

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <old_dir> <new_dir>\n";
my $old = shift or die $usage;
my $new = shift or die $usage;

my %current = ();

davetang

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <infile.bed>\n";
my $infile = shift or die $usage;

my %bed = ();

davetang

#!/bin/env perl

use strict;
use warnings;

#hash for filehandles
my %fh = ();

#read from stream
while (<>){

davetang

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <bam_flag>\n";
my $flag = shift or die $usage;

die "Please enter a numerical value\n" if $flag =~ /\D+/;

davetang

#!/usr/bin/perl

use warnings;
use strict;

my $BAILOUT=16;
my $MAX_ITERATIONS=1000;

my $begin = time();