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/ggbeeswarm
Column scatter / beeswarm-style plots in ggplot2
eclarke/swga
Select primer sets for selective whole genome amplification (SWGA)
eclarke/komplexity
A method of assessing sequence complexity based on kmer frequencies
eclarke/linecount
Fast, simple line count function in Rust
eclarke/mars
MARS - MinION Assembly and Reporting System
eclarke/eclectic
random R functions
eclarke/argutils
Python utility for converting between config files and argument parsers
eclarke/fqscan
Scans a directory of (optionally paired) FASTQ files for the prevalence of particular targets
eclarke/harb-modeling
Hierarchical, autoregressive binomial models for microbiome data
eclarke/jrdcolors
Fill and color scales for ggplot2, adapted from JRD suggested colors
eclarke/s3sync
Sync directory with an S3-compatible endpoint
eclarke/github_tutorial
A hands on forking, cloning, pulling, pushing, merging tutorial.
eclarke/Deepbinner
a signal-level demultiplexer for Oxford Nanopore reads
eclarke/dotfiles
the usual, just some dotfiles
eclarke/eclarke
Config files for my GitHub profile.
eclarke/kraken-biom
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
eclarke/krakenhll
KrakenHLL metagenomics classification method with unique k-mer counting for more specific results
eclarke/kz_conda
Conda recipe for komplexity (https://github.com/eclarke/komplexity/)
eclarke/metaglomr
Tools for tidy metagenomics
eclarke/mira-diversity
Modeling diversity attributable to exposure to antibiotics in an LTACH cohort
eclarke/ori
An interactive FITS file explorer and organizer
eclarke/rust-bio-tools
A set of command line utilities based on Rust-Bio.
eclarke/sbx_rgi
Sunbeam extension to run RGI (Resistance Gene Identifier)
eclarke/sbx_rgi5
Sunbeam extension for RGI v5
eclarke/sbx_template
Template for Sunbeam extensions.
eclarke/scid-multiomics-paper
Figures and tables for the SCID-X1 multiomics paper
eclarke/shortbred-snakemake
Rules to run ShortBRED using Snakemake
eclarke/venus
Illumina Bacterial WGS QC and Assembly Pipeline (companion to MARS)
eclarke/website
Source code for eclarke.github.com
eclarke/workspace-configs