eclarke

ggbeeswarm

Column scatter / beeswarm-style plots in ggplot2

eclarke

Config files for my GitHub profile.

ori

An interactive FITS file explorer and organizer

workspace-configs

jrdcolors

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

github_tutorial

A hands on forking, cloning, pulling, pushing, merging tutorial.

mars

MARS - MinION Assembly and Reporting System

venus

Illumina Bacterial WGS QC and Assembly Pipeline (companion to MARS)

sbx_rgi5

Sunbeam extension for RGI v5

swga

Select primer sets for selective whole genome amplification (SWGA)

argutils

Python utility for converting between config files and argument parsers

linecount

Fast, simple line count function in Rust

sbx_rgi

Sunbeam extension to run RGI (Resistance Gene Identifier)

Deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

mira-diversity

Modeling diversity attributable to exposure to antibiotics in an LTACH cohort

harb-modeling

Hierarchical, autoregressive binomial models for microbiome data

metaglomr

Tools for tidy metagenomics

sbx_template

Template for Sunbeam extensions.

s3sync

Sync directory with an S3-compatible endpoint

komplexity

A method of assessing sequence complexity based on kmer frequencies

kz_conda

Conda recipe for komplexity (https://github.com/eclarke/komplexity/)

dotfiles

the usual, just some dotfiles

kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

rust-bio-tools

A set of command line utilities based on Rust-Bio.

krakenhll

KrakenHLL metagenomics classification method with unique k-mer counting for more specific results

fqscan

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

eclectic

random R functions

shortbred-snakemake

Rules to run ShortBRED using Snakemake

scid-multiomics-paper

Figures and tables for the SCID-X1 multiomics paper

website

Source code for eclarke.github.com