Erik Clarke

ggbeeswarm. Column scatter / beeswarm-style plots in ggplot2

swga. Select primer sets for selective whole genome amplification (SWGA)

komplexity. A method of assessing sequence complexity based on kmer frequencies

melt. Standalone nucleotide sequence melt temp calculator for Python

linecount. Fast, simple line count function in Rust

mars. MARS - MinION Assembly and Reporting System

sarcoid-microbiome-paper. Code to generate figures, etc for the Clarke et al sarcoid microbiome paper

ncbi-baltimore. Gets the Baltimore ranks (if applicable) from NCBI taxa IDs

oboparser. Parses GO OBO files, with (limited) reasoning

eclectic. random R functions

refseq_dl. Download refseq genomes for a group using Snakemake

onecodex_pipeline. Pipeline for parsing One Codex analyses

jrdcolors. Fill and color scales for ggplot2, adapted from JRD suggested colors

config. Erik's Config Files

fqscan. Scans a directory of (optionally paired) FASTQ files for the prevalence of particular targets

swga_paper. Data and analysis for the SWGA paper

go-historical-analysis. Pipeline for the mass analysis of GEO datasets using historical versions of the Gene Ontology annotations.

argutils. Python utility for converting between config files and argument parsers

tomorrow-theme. Colour Schemes for Hackers

s3sync. Sync directory with an S3-compatible endpoint

biopython. Official git repository for Biopython (converted from CVS)

blog. blog

mwsync. Java framework to create live mirrors of MediaWiki sites.