Erik Clarke (eclarke)

eclarke

Geek Repo

Company:Janssen Research & Development

Location:Philadelphia, PA

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Organizations
sunbeam-labs

Erik Clarke's repositories

ggbeeswarm

Column scatter / beeswarm-style plots in ggplot2

swga

Select primer sets for selective whole genome amplification (SWGA)

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komplexity

A method of assessing sequence complexity based on kmer frequencies

diceware

python implementation of diceware (using os.urandom)

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linecount

Fast, simple line count function in Rust

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mars

MARS - MinION Assembly and Reporting System

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argutils

Python utility for converting between config files and argument parsers

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eclectic

random R functions

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fqscan

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

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harb-modeling

Hierarchical, autoregressive binomial models for microbiome data

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jrdcolors

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

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s3sync

Sync directory with an S3-compatible endpoint

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github_tutorial

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

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Deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

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dotfiles

the usual, just some dotfiles

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kraken-biom

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

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krakenhll

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

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kz_conda

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

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metaglomr

Tools for tidy metagenomics

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mira-diversity

Modeling diversity attributable to exposure to antibiotics in an LTACH cohort

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rust-bio-tools

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

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sbx_rgi

Sunbeam extension to run RGI (Resistance Gene Identifier)

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sbx_rgi5

Sunbeam extension for RGI v5

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sbx_template

Template for Sunbeam extensions.

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scid-multiomics-paper

Figures and tables for the SCID-X1 multiomics paper

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shortbred-snakemake

Rules to run ShortBRED using Snakemake

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venus

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

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website

Source code for eclarke.github.com

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