audy

#!/usr/bin/env ruby

#
# Compute Shannon Diversity Index from a CSV file
# Input has samples as columns, variables as rows
#
#
# (c) 2014 Austin G. Davis-Richardson
# LICENSE: MITv3

audy

Option Parsing in R

Using: https://github.com/trevorld/optparse

hello.R

#!/usr/bin/env Rscript

library(optparse)

audy

Keybase proof

I hereby claim:

• I am audy on github.
• I am audy (https://keybase.io/audy) on keybase.
• I have a public key whose fingerprint is ECAA 9A28 758A BB1F 77CD 2299 6707 68C1 407B E56C

To claim this, I am signing this object:

audy

audy

Classifier: RDP Naive Bayesian rRNA Classifier Version 2.6, Sep 2013 
Taxonomical Hierarchy: RDP 16S rRNA training set 9
Query File: bacteroides-sequences.fasta
Submit Date: Wed Apr 23 16:53:26 EDT 2014
Confidence threshold (for classification to unclassified_"Porphyromonadaceae" ONLY): 80%
Symbol +/- indicates predicted sequence orientation

821498;+;Bacteria;100%;"Bacteroidetes";100%;"Bacteroidia";100%;"Bacteroidales";100%;"Porphyromonadaceae";98%;Tannerella;65%
729992;+;Bacteria;100%;"Bacteroidetes";100%;"Bacteroidia";100%;"Bacteroidales";100%;"Porphyromonadaceae";100%;Dysgonomonas;62%
637013;+;Bacteria;100%;"Bacteroidetes";100%;"Bacteroidia";100%;"Bacteroidales";100%;"Porphyromonadaceae";100%;Dysgonomonas;60%

audy

var shell = require('mesh-viewer')();
var vport = require('gl-viewport')(shell, { viewMode: 'ortho' });
 
window.addEventListener('keydown', function (ev) {
    if (String.fromCharCode(ev.which) === 'P') {
        var mode = vport.viewMode === 'ortho' ? 'perspective' : 'ortho';
        vport.setViewMode(mode);
    }
});
 

audy

#!/usr/bin/env Rscript

foo

audy

file_to_disk = './tmp/large_disk.vdi'

Vagrant::Config.run do |config|
  config.vm.box = 'base'

  config.vm.customize ['createhd', '--filename', file_to_disk, '--size', 500 * 1024]
  config.vm.customize ['storageattach', :id, '--storagectl', 'SATA Controller', '--port', 1, '--device', 0, '--type', 'hdd', '--medium', file_to_disk]
end

audy

#!/usr/bin/env Rscript

library(phyloseq)
library(magrittr)

data(GlobalPatterns)

GlobalPatterns %>%
  ordinate('NMDS', 'bray') %>%
  plot_ordination(GlobalPatterns, ., type='split', color='Phylum', label='SampleType')

audy

#!/usr/bin/env ruby

require 'csv'

translation = CSV.read(ARGV[0])

translation.map! { |x| [/#{x[0]}/, x[1]] }

d = File.read('/dev/stdin')