Discover audy/make-rmarkdown Open Source project

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Rank 1,909,155 (Top 39 %)
Language Makefile
License
MIT License
Created over 9 years ago
Updated about 8 years ago

audy

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Make + RMarkdown for minimally replicable scientific computing.

domain-name-generator

generat.es clev.er sho.rt doma.in nam.es

Python

bioinformatics-hacks

Scripts for miscelleneous bioinformatics tasks

Python

catsay

🐱 💻 like cowsay but cats

Ruby

stitch

Overlap assembler of paired-end DNA sequences generated by Illumina

Python

memelicious

Parser of internet memes

Ruby

smalldata

Small(-ish) datasets for fun and teaching

taxcollector

16S rRNA database

Python

miseq-16S-pipeline

HPC pipeline for overlapping V4 16S rRNA reads generated on Illumina MiSeq

Python

tbl2asn-forever

Use tbl2asn forever by pretending that it's still 2019

Dockerfile

lederhosen

User-friendly tool to quickly go from 16S rRNA sequence data to an OTU matrix

Ruby

evernote-git-backup

Automatically backup Evernote notes to HTML files and track using Git

AppleScript

dotflies

~ bleep bloop

Vim Script

ncbi-taxonomy-bot

Bot that tweets when NCBI updates their taxonomy database

Python

barcode-generator

Generate nucleotide sequences for multiplexed sequencing aka "barcoding" given some constraints.

Python

esrapgra

The opposite of argparse

Python

genome-explorer

🔬 Genome Browser for Bacteria

Ruby

telegram-bot

🤖 ☎️ it's a me! telegram bot!

Python

cram

Comparative, Rapid Analysis of Metagenomes

Python

dna

A biological sequence file (fasta, fastq, qseq) parser for Ruby

Ruby

craigslist-twitter-bot

Craigslist-scraping Twitter bot

Ruby

downloads

💾 Happy file downloading for Python

Python

bioinformatics

annotated list of bioinformatics tools I used

tree-of-life

🌳 API for NCBI taxonomic lineages

Ruby

deskclean

Keep your ~/Desktop tidy!

media-recipes

food for microbes

vagrant-torque

Run a single machine torque cluster inside of a Vagrant VM.

Shell

presentations

My presentations and talks

Ruby

docker-sciruby-notebook

SciRuby + IRuby notebook in a Docker container

poster-session-bootstrap

Create academic style posters by editing markdown files. Focus on content instead of layout.

Ruby

I took this class and got a B

galaxy-illumina-16S

Ion Torrent 16S rRNA amplicon pipeline for Galaxy

Python

tiny-tax

A small lib for names/nodes.dmp

Python

R-IRC

The IRC line client protocol in R

pipet

Bioinformatics Database "Package Manager"

Ruby

deutsch-bot

Ruby IRC bot to teach myself German

Ruby

greenhouse-monitor

Code and specs for a remote, always-on (3G), temperature and humidity sensor running on a Raspberry Pi

JavaScript

Forage

grep for nucleotides

Ruby

hiseq-16s-pipeline

Process Illumina 16S amplicons on the really big computer at the University of Florida

Python

cd-hit-that

Python

sqlalchemy-sandbox

Thing I made to get good at SQLAlchemy

Python

wrapperer

A universal wrapper for command line programs in R

banana

A tool for handling multiplexed 454 and Illumina generated sequence data

klotzbot

bitbars

pass-app

A simple, web-based front-end for password-store

Ruby

bio-dat

Examples/experiments of using dat with bioinformatics (sequence) data.

JavaScript

bart-analysis

🚉 Analyzing BART data

Jupyter Notebook

pangea

taxonomy-dependent short read 16S rRNA classifier

Perl

hdf5-dna

Examples and experiments of using HDF5 and h5py with biological sequence data

Python

rrna_validation

Final Project for ZOO6927 - Methods of Phylogenetic Inference

Ruby

Grape

Distributed BLAST

Ruby

import-sequences

Horrifying hack for importing raw DNA sequencing reads into a standard format

Ruby

tilde

things related to tilde.town

HTML

crosswords

📰 ☕ crossword puzzle generator

Python

miniblast

The usual seed and extend search algorithm implemented in Ruby.

Ruby

phylograph

Project for a class

Ruby

python-science-skeleton

IPython data science project skeleton

Makefile

berkeley-bowl-soups

Scraping and analyzing the daily soup offerings at Berkeley Bowl

Python

falafel.space

🔨 A Minecaft Server

Shell

bio-xl

Tools for dealing with large (> memory) collections of nucleotide sequences

Python

clump

Another class project

Python

speck-notebook

so I can run speck on binder

Jupyter Notebook

Dockerfiles

@audy's dockerfiles

scratch

👾 I program my home computer

audy.github.io

learning-rust

pangea3

OTU clustering pipeline based on CLC Assembly Cell

Perl

audy

plottery

Procedurally Generated Pottery

Jupyter Notebook

miniblog

mini tiny bloggy thingy

HTML

sequence-storage

web app for managing lots of sequence data

Ruby

self.check

Keep track of self-reported data about yourself.

Python

audy/make-rmarkdown

audy

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