spacocha,github

16s_pre-processing_scripts

Scripts needed to process raw sequence data files

assessing-genetic-predictors-of-antibiotic-resistance-phenotypes

Code used to analyze the antibiotic resistance genotype-phenotype relationship in wastewater Pseudomonas isolates

beagle_bin

Personal repo with a random collection of scripts

bottle_mixing_model

Simple box model to predict mixing in bottles

chesapeakebay_shotgun_metagenomics

Scripts and pipeline associated with the shotgun metagenomic analysis of samples from 2017 in the Chesapeake Bay

chesapeakesulfuroxidation

Scripts associated with manuscript submitted to Environmental Microbiology

class_moving_pictures_pipeline

Scripts for running moving pictures tutorial on MARCC

Extremely accurate algorithm used to group DNA sequences from microbial communities into operational taxonomic units (proxy for species) for ecological or biomedical research. This algorithm uses the information contained in the distribution of DNA sequences across samples along with sequence distances to cluster sequences accurately.

distribution-based-clustering

Extremely accurate algorithm used to group DNA sequences from microbial communities into operational taxonomic units (proxy for species) for ecological or biomedical research. This algorithm uses the information contained in the distribution of DNA sequences across samples along with sequence similarity to cluster sequences more accurately than other methods that are currently available. Developed for Illumina next-generation sequencing libraries, but applicable to any sequencing platform with sufficient number of counts per sample to infer distribution patterns.

epicpcr_sequence_extraction

Scripts for processing epicPCR data

fa19_methods_git

This is a test repository for the class to learn to use gits and github.

fa19_moving_picture_repository

This is a repository for Methods in Microbial Community Analysis for pipeline development for the moving pictures analysis

fa21_methods_git

fa_esakows1_146632

fdafm

genome_biogeo

Genome explicit biogeochemical model. Combination of models, such as Mystic (Preheim et al), GENOME (Coles et al) and gene-centric approached of Reed et al and Louca et al.