kdaily

################################################################################
# Copyright 2011
# Andrew Redd
# 11/23/2011
#
# Description of File:
# Makefile for knitr compiling
# 
################################################################################
all:pdf  # default rule DO NOT EDIT

kdaily

## Need plyr
require(plyr)

## Some fake data
foo <- data.frame(a=rep("foo", 3), b=rep("foofoo", 3), c=rep("foobarfoo", 3))

## Replace function, works on vectors
fn <- function(x) gsub("foo", "bar", x)

## Turn it into a column-wise function; only apply to cols "a" and "b"

kdaily

This post examines the features of [R Markdown](http://www.rstudio.org/docs/authoring/using_markdown) 
using [knitr](http://yihui.name/knitr/) in Rstudio 0.96.
This combination of tools provides an exciting improvement in usability for 
[reproducible analysis](http://stats.stackexchange.com/a/15006/183).
Specifically, this post 
(1) discusses getting started with R Markdown and `knitr` in  Rstudio 0.96;
(2) provides a basic example of producing console output and plots using R Markdown;
(3) highlights several code chunk options such as caching and controlling how input and output is displayed;
(4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and 
(5) discusses the implications of R Markdown.

kdaily

#!/usr/bin/env python
# split a bam file by read group ID
# Sean Davis <seandavi@gmail.com>
# March 10, 2012
# 
import pysam
import argparse
import logging

logging.basicConfig(level=logging.INFO)

kdaily

"""Add the read group ID to each read name in a BAM or SAM file.

Must output to SAM format to get the header.

To directly convert to BAM, pipe to samtools view:

python add_rgid_to_qname.py INPUT.sam /dev/stdout | samtools view -Sb /dev/stdin > OUTPUT.bam

"""

kdaily

def safe_qsub_run(cmd, jobname, script_header=_script_header, nodes=1, params="", stdout=None, stderr=None, shell=False):
    """Run a command via qsub in blocking mode so that the command waits to exit.
       Requires a header string and a job name.
    """
    
    scriptfile = tempfile.NamedTemporaryFile()
    scriptfile.write("%(header)s\n%(command)s\n" % dict(header=script_header, command=cmd))
    scriptfile.file.flush()
    
    qsub_cmd = "qsub -N %(jobname)s -l nodes=%(nodes)s -W block=true %(params)s" % dict(jobname=jobname,

kdaily

# Read .mp3 files from a given directory, compare songs, and play them in order of similarity
# To run, source this file, then:
# arrangeMusicC(inDirectory = getwd())

library("plyr")
library("tuneR")
library("seewave")

library("compiler")

kdaily

GGGGCTCCTAGCCTCCGAGGCCTCTGGAAAAAAAAGAGAGAGGCCTCTGAGGCTTAAGAGGCTTAATTAGCAAAAAAGGCAGTATCTAAGGGCAGATCCCAAGGGCGGGAAACTGCAGTATAAAAACCACTCCTTAGTGAGGTAGCTCATTTGCTCCTCTGCTCTTTCTGCAAACTCCTTCTGCATATAGACAAGATGGATTTAGTCCTAAATAGGAAAGAAAGAGAGGCTCTCTGCAAGCTTTTAGAGATTGCTCCTAATTGTTATGGCAACATCCCTCTGATGAAAGCTGCTTTCAAAAGAAGCTGCTTAAAGCATCACCCTGATAAAGGGGGAAATCCTGTTATAATGATGGAATTGAACACCCTTTGGAGCAAATTCCAGCAAAATATCCACAAGCTCAGAAGTGACTTCTCTATGTTTGATGAGGTCAGTACAAAATTTCCTTGGGAAGAATATGGAACTTTAAAGGATTATATGCAAAGTGGATATAATGCTAGATTTTGCAGAGGTCCTGGGTGCATGCTTAAGCAACTTAGAGATTCTAAGTGCGCTTGTATTAGCTGTAAGTTGTCTCGCCAGCATTGTAGTCTAAAAACTTTAAAGCAAAAAAACTGTCTGACGTGGGGAGAGTGTTTTTGCTATCAGTGCTTTATTCTTTGGTTTGGATTTCCTCCTACTTGGGAAAGTTTTGACTGGTGGCAAAAAACTTTAGAAGAAACTGACTACTGCTTACTGCATCTGCACCTTTTCTAGACTCCTACTTCCTTCCTCTGTAAGTATTAGATATGGAAAAGTCTATAAGGCAAAATATCAAAGAAAGGTTATTTATGACAGATTTTCTGTACTTTCCCATCTAGGTTGACGAGGCCCCTATATATGGGACCACTAAATTCAAAGAATGGTGGAGATCAGGAGGATTCAGCTTCGGGAAGGCATACGAATATGGGCCCAATCCACACGGGACCAACTCAAGATCCAGAAAGCCTTCCTCCAATGCATCCAGGGGAGCCCCCAGTGGAAG

kdaily

NIH research festival
========================================================

http://researchfestival.nih.gov/2013/posters.cgi

chrom-4
Cancer-4
Cancer-5
Molbio-6

kdaily

#!/usr/bin/perl -w

# From http://genomics-pubs.princeton.edu/prv/resources/scripts/fastq-filter_extract_reads.pl

=head1 NAME

fastq-filter_extract_reads.pl - Splits fastq file based on read ids in a list 

=head1 SYNOPSIS