elizabethmcd

metabolisHMM

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs

genomes-MAGs-database

Creation of a database of Genbank genomes including isolate reference genomes and MAGs, and parallelizing 1000s of genome searches for a specific marker

MEHG

Exploring the phylogenetic and metabolic diversity of microbial mercury methylation

elizabethmcd.github.io

Personal website built with Quarto

R3R4

Metagenomic assembly and metatranscriptomic analysis of co-occuring Accumulibacter populations

EBPR-MAGs

Extracting, refining, and utilizing MAGs from EBPR reactor metagenomic time-series

ppk1_Database

Repository for assigning Accumulibacter clade designations based on ppk1 nomenclature

2019-06-27-REU-DataCarpentry

Slides and R code for teaching Intro to R for REU Data Carpentry @ UW-Madison on 2019-06-27

Abigail_EBPR_SBR

Microbial community analysis of a lab-scale SBR simulating EBPR

AcDiv

Microdiversity and population structure of Accumulibacter using genome-resolved metagenomics

algaeLakes

Searching for algae in Lake Mendota time series collab

arcadia-docker-builds

Glossary of Docker builds that are either maintained or used by Arcadia

cv

Elizabeth McDaniel CV

genomeassembler

github-pages-intro

Lesson materials for creating a personal website with Github Pages

infant_gut_microbiome

Transposons in the infant gut microbiome analysis

Lake-MAGs

Reassembly and binning of lake metagenomes from GEODES, MEHYPO, and the historical time-series metagenomics projects

mcfaModule

Teaching module on genome-resolved metagenomic binning

metaG-bin-analysis

MicDiv

Comparisons of microbial diversity within lab-scale and full-scale EBPR systems

obscurePOS

Genome-resolved metagenomics of photosynthetic EBPR

R-amplicons

Course website for MICRO 551 lessons on analyzing amplicon data in R

R1PopDynamics

Population dynamics at multiple scales of resolution of engineered bioreactor ecosystems

resources

Curated lists of resources for learning coding, bioinformatics, metagenomics, etc.

Sakinaw

Metagenomic and metatranscriptomic analysis of anoxic communities in Lake Sakinaw, BC

SAOB

Metabolic networks of a syntrophic-acetate oxidizing lab-scale bioreactor community

TbasCO

teaching

Slide decks and scripts for teaching workshops

tfdA

Diversity and Distribution of tfdA marker underpinning microbial 2,4-D degradation

uTR

Detect key Units in mosaic Tandem Repeats from representative reads from the same locus