eclarke
Data scientist with an interest in developing free/open-source tools for scientific research.
Janssen Research & DevelopmentSan Diego, CA
Pinned Repositories
eclectic
random R functions
ggbeeswarm
Column scatter / beeswarm-style plots in ggplot2
komplexity
A method of assessing sequence complexity based on kmer frequencies
linecount
Fast, simple line count function in Rust
mars
MARS - MinION Assembly and Reporting System
melt
Standalone nucleotide sequence melt temp calculator for Python
ncbi-baltimore
Gets the Baltimore ranks (if applicable) from NCBI taxa IDs
sarcoid-microbiome-paper
Code to generate figures, etc for the Clarke et al sarcoid microbiome paper
swga
Select primer sets for selective whole genome amplification (SWGA)
sunbeam
A robust, extensible metagenomics pipeline
eclarke's Repositories
eclarke/ncbi-baltimore
Gets the Baltimore ranks (if applicable) from NCBI taxa IDs
eclarke/sarcoid-microbiome-paper
Code to generate figures, etc for the Clarke et al sarcoid microbiome paper
eclarke/oboparser
Parses GO OBO files, with (limited) reasoning
eclarke/onecodex_pipeline
Pipeline for parsing One Codex analyses
eclarke/refseq_dl
Download refseq genomes for a group using Snakemake
eclarke/swga_paper
Data and analysis for the SWGA paper
eclarke/amos-conda
Conda package for AMOS
eclarke/brocc
Consensus taxonomy assignment for short reads (great for fungi)
eclarke/clark_scripts
Scripts for CLARK to facilitate deployment
eclarke/CondaIntro
Introduction to using conda
eclarke/decontam
eclarke/dsk-conda
Conda recipe for DSK 1.6906
eclarke/dsk-rs
A reimplementation of DSK (Rizk et al. 2013) in Rust
eclarke/eclarke.github.io
eclarke/eclpalettes
Qualitative color palette toolkit for R
eclarke/fastx
Speedy FASTA/FASTQ library and toolkit
eclarke/forcats
🐈🐈🐈🐈: tools for working with categorical variables (factors)
eclarke/fqfa-rs
Simple, quick FASTQ to FASTA converter
eclarke/idba
eclarke/idba-conda
Bioconda recipe for IDBA
eclarke/kmer-rs
k-mer counting in Rust, generalized over all lengths of k
eclarke/mindb
Minimal Kraken database, for testing
eclarke/pipits
eclarke/prezto
The configuration framework for Zsh
eclarke/qiimer
Quantitative Insights Into Microbial Ecology - parsing and plotting functions for R
eclarke/scid_virome_analysis
Virome of SCID-X1 patients
eclarke/set_finder
A modified version of cliquer for use with SWGA
eclarke/sisyphus
enSemble In-silico aSsembly of PHage Und Similar
eclarke/sunbeam-data
Test data for the sunbeam pipeline
eclarke/swga-conda
conda recipe for SWGA