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2017_aem_figure_s2

Interactive plots of NMDS results

bactaxr

Bacterial taxonomy construction and evaluation in R

besplot

Interactive PCA and NMDS plots

bgc_workshop

Materials for the BGC detection workshop

bioconda-recipes

Conda recipes for the bioconda channel.

bminer

A companion application for analyzing and viewing BTyper output files in aggregate

brisk

Bacillus cereus exposure/evaluation of risk (beta)

btyper

Rapid, in silico characterization of Bacillus cereus group isolates using WGS data

btyper3

In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data

fsl_wgs_pipeline

Whole-genome sequencing quality control and assembly pipeline

group_iii_bacillus_cereus

Supplementary material for the 2019-2020 cereulide-producing Group III B. cereus s.l. phylogenomics study

homebrew-btyper

homebrew-btyper-testing

homebrew-btyper3

Homebrew formula for BTyper3

homebrew-core

🍻 Default formulae for the missing package manager for macOS

homebrew-seq2mlst

Tap for seq2mlst (in silico MLST tool)

homebrew-snpbac

jfp_sublethal_heat_stress_modeling

Statistical analyses conducted for Journal of Food Protection sublethal heat stress modeling paper

lrnrisk

Materials for the LRNRisk project

nys_typhimurium_2018

Supplementary material for the 2018 New York state Typhimurium project

rna_seq_workshop_uzh_2017

Materials for the RNA-Seq Data Analysis Workshop at the University of Zurich, February 16, 2017

rna_seq_workshop_uzh_2018

Materials for the RNA-Seq Data Analysis Workshop at the University of Zurich, April 6, 2018

scriptcity

Random (meta)genomics/(meta)transcriptomics-related scripts

seq2mlst

In silico multi-locus sequence typing (MLST) for bacterial genomes

skylinetools

Utilities and distributions for (birth-death) skyline models.

snpbac

SNP and variant calling pipeline for bacteria

ubc_wgs_workshop_2019

Materials for the bacterial whole-genome sequencing data analysis workshop at the University of British Columbia, April-May 2019

zru_farms

Supplementary data for the ZRU Farms Salmonella project