CD2H gitForager

Austin Richardson

Login: audy

Company: @pivotbio

Location: San Francisco, CA

Bio: ?????

Blog: http://agdr.org

Member of

Repositories

audy.github.io: http://agdr.org
awesome-public-datasets: An awesome list of (large-scale) public datasets on the Internet. (On-going collection)
banana: A tool for handling multiplexed 454 and Illumina generated sequence data
barcode-generator: Generate nucleotide sequences for multiplexed sequencing aka "barcoding" given some constraints.
bart-analysis: :station: Analyzing BART data
berkeley-bowl-soups: Scraping and recording the daily soup offerings at Berkeley Bowl
bfc: Move along. Nothing to see here.
bio-dat: Examples/experiments of using dat with bioinformatics (sequence) data.
bioinformatics: annotated list of bioinformatics tools I used
bioinformatics-hacks: Scripts for miscelleneous bioinformatics tasks
biom-format: The Biological Observation Matrix (BIOM) Format Project
bio-xl: Tools for dealing with large (> memory) collections nucleotide sequences
bitbars: my bitbar plugins
blamer: Blamer adds userstamps to ActiveRecord models
bleep-bloop: Procedurally generated, therapeutic bleeps and occasionally bloops
bots: :robot: bleep bloop
box: null
C: I took this class and got a B
capp-stories: Source of http://twitter.com/cappstories
catsay: :cat: :computer: Cats in your $SHELL
cd-hit-that: null
cheatsheets: null
clump: Another class project
containers: Bioinformatics containers
corpora: A collection of small corpuses of interesting data for the creation of bots and similar stuff.
craigslist: Unofficial mirror/fork of the now defunct Craigslist RubyGem.
craigslist-twitter-bot: Craigslist-scraping Twitter bot
cram: Comparative, Rapid Analysis of Metagenomes
data-1033-program: Agency-level data current to November 14, 2014. Source: Department of Defense, Defense Logistics Agency.
datasets: My datasets
dbbp: DataBase of Bacterial Phenotypes
ddmp: Digital Database of Microbial Phenotypes. Like an online Bergey's Manual.
deskclean: Keep your ~/Desktop tidy!
deutsch-bot: Ruby IRC bot to teach myself German
dna: A biological sequence file (fasta, fastq, qseq) parser for Ruby
docker-A5-miseq: a docker container for benchmarking A5-miseq in nucleotid.es
Dockerfiles: @audy's dockerfiles
docker-homely-mutt: :envelope: :dog: The Homely Mutt by @sjl in Docker form
docker-jbrowse: Docker recipe for JBrowse (web-based genome browser)
docker-jbrowse-1: Docker image of JBrowse Genome Browser
docker-kraken: null
docker-password-store: Run password-store and GnuPG inside of a Docker container
docker-picrust: Run PICRUST inside of a Docker container
docker-sciruby-notebook: SciRuby + IRuby notebook in a Docker container
docker-uclust: UCLUST in Docker
docker-uptime: A dockerized Uptime Container
dokku-buildpack-jekyll3-nginx: Jekyll 3 on Dokku
domain-name-generator: generat.es clev.er sho.rt doma.in nam.es
dos-and-donts: Scrape the DOs and DONTs from VICE
dotflies: my ?
downloads: :floppy_disk: Simpler file downloading for Python
esrapgra: The opposite of argparse
evernote-git-backup: Automatically backup Evernote notes to HTML files and track using Git
faker: A library for generating fake data such as names, addresses, and phone numbers.
falafel-renderer: Scripts to generate https://falafel.space map
falafel.space: :hammer: A Minecaft Server
figtree: null
Forage: grep for nucleotides
gainesville-open-data: Data from the Gainesville, FL open data portal
galaxy-illumina-16S: Ion Torrent 16S rRNA amplicon pipeline for Galaxy
genome: Genomes, represent!
genome-explorer: :microscope: Social network for Bacteria
genome-pipeline: Bacterial genome processing filters and utilities based on HTML-Pipeline
ggpy: ggplot port for python
good_puppeRs: Downloading rated dog pictures from @dog_rates
Grape: Distributed BLAST
greenhouse-monitor: Code and specs for a remote, always-on (3G), temperature and humidity sensor running on a Raspberry Pi
guestbook: fork me and leave a message
hdf5-dna: Examples and experiments of using HDF5 and h5py with biological sequence data
heroku-buildpack-multi: DEPRECATED: Composable buildpacks
hiseq-16s-pipeline: Process Illumina 16S amplicons on the really big computer at the University of Florida
homebrew-formulae: Personal Homebrew Formulae
homebrew-science: :microscope: Scientific formulae for the Homebrew package manager
hpc-monitor: monitor status of jobs on a high-performance compute cluster with sounds
import-sequences: Horrifying hack for importing raw DNA sequencing reads into a standard format
irc: A simple go irc library meant to be a building block for other projects
jbrowse: A modern genome browser built with JavaScript and HTML5.
klotzbot: IRC bot that logs
kraken: Kraken taxonomic sequence classification system
lai-2015: scripts for Lai 2015
la-microbioma: Listen to the beautiful music of the microbiome!
lederhosen: User-friendly tool to quickly go from 16S rRNA sequence data to an OTU matrix
le-painting: A social network for doodling. Source of http://painting.austinfanclub.com
magnus: A bot to remind me of my own mortality (and other useful facts such as the weather)
mailcrow: :bird: escrow for email
make-rmarkdown: Make + RMarkdown for minimally replicable scientific computing.
markov_inspiration: Markov chains and corpuses for your enjoyment.
media-recipes: food for microbes
memelicious: Parser of internet memes
miniblast: The usual seed and extend search algorithm implemented in Ruby.
miniblog: mini tiny bloggy thingy
mirror-casot.pl: mirror/fork of CasOT
miseq-16S-pipeline: HPC pipeline for overlapping V4 16S rRNA reads generated on Illumina MiSeq
monsterid: Generates cute little monsters from text
nearproteins: :mag: :book: Amino Acids Database with Fuzzy Querying
neiss: Data from National Electronic Injury Surveillance System
OrthoMCL: null
our-boxen: Copy me for your team.
over9000: 9001.over_9000?
pangea: taxonomy-dependent short read 16S rRNA classifier
pangea3: OTU clustering pipeline based on CLC Assembly Cell
PaperBadger: Exploring the use of digital badges for crediting contributors to scholarly papers for their work
pass-app: A simple, web-based front-end for password-store
phd: My PhD Dissertation
phone-blast: source code for the original BLAST server
phony: prints combinations of words that can be generated by the same numbers on a dial-pad and "predictive text"
phylograph: Project for a class
phyloseq-data: A collection of microbiome datasets for Phyloseq
phyloseq-time: Functions for analyzing microbiome data across a time variable - A Phyloseq extension
pipet: Bioinformatics Database "Package Manager"
pomodoro.sh: yet another pomodoro timer
poster-session-bootstrap: Create academic style posters by editing markdown files. Focus on content instead of layout.
presentations: My presentations and talks
prokka: Rapid prokaryotic genome annotation
python-science-skeleton: IPython data science project skeleton
rb-gsl-1: rb-gsl for NMatrix
recurrentshop: Framework for building complex recurrent neural networks with Keras
riboparty: null
richardson-2014: Analysis code for the DIPP microbiome study
r-imgur: R graphics device that uploads to imgur
R-IRC: The IRC line client protocol in R
RMagick4J: RMagick for JRuby.
roda: Routing Tree Web Toolkit
rpi: My Raspberry PI Setup
rrna_validation: Final Project for ZOO6927 - Methods of Phylogenetic Inference
rspec-rails: RSpec for Rails-3+
ruby-dmtx: Libdmtx wrapper gem for ruby
schoolbus: A python library for checking if an email is issued by an academic institution. Useful for granting discounts, etc to academic users.
scratch: :space_invader: I program my home computer
self.check: Keep track of self-reported data about yourself.
sequence-manipulation-suite: fork of the sequence-manipulation-suite [with Docker]
sequenceserver: Intuitive local web frontend for the BLAST bioinformatics tool
sequence-storage: web app for managing lots of sequence data
sharkbot: Grooveshark IRC bot
sinatra: Classy web-development dressed in a DSL (official / canonical repo)
skellington: :skull: World's Greatest Sinatra Skeleton
smalldata: Small(-ish) datasets for fun and teaching
snpr: The sources of the openSNP website
SomePackage: Python package boilerplate with unit testing and setuptools.
spirulina: null
stitch: Assembler of paired-end DNA sequences generated by Illumina
sunny_bot: IRC weather bot
supreme-happiness: Reformatter/prettifier for multiple languages
taxcollector: 16S rRNA database
telepooz: Functional Telegram Bot API wrapper for Scala on top of akka, circe, cats, and shapeless
terra: :space_invader: JS library for simple biological simulations and cellular automata
test-app: testing setting up CI
thrash: Randomly write to many, many files. Created out of ignorance and desperation.
tilde: things related to tilde.town
traitar: null
tree-of-life: :deciduous_tree: API for NCBI taxonomic lineages
uniprot: retrieve protein sequence identifiers and metadata from http://uniprot.org
vagrant-galaxy: Vagrant launcher for Galaxy
vagrant-rstudio: Yet another Vagrantfile for RStudio
vagrant-torque: Run a single machine torque cluster inside of a Vagrant VM.
which_is_the_fastest: Which is the fastest web framework?
wieso: wieso
wrapperer: A universal wrapper for command line programs in R
yolo-hipster: Naive Bayes taxonomy classifier using scikit-learn

Commits To

Repository	Most Recent Commit	# Commits
audy/bioinformatics-hacks	2018-01-04 23:36:26.0	128
audy/genome-explorer	2017-03-02 02:48:28.0	532
audy/bioinformatics	2016-05-20 04:15:22.0	5

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.