elizabethmcd Goto Github PK

2019-05-19-glbio-docker

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

ani_compare_dag

Directory setup to run mass ani comparisons on HTcondor system

arcadia-docker-builds

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

blast-dagman

Directed Acyclic Workflow Manager for running BLAST all-v-all on HTCondor

cci

Instructions and shell scripts for configuration and setup of CCI VM

cv

Elizabeth McDaniel CV

ebpr-mags

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

elizabethmcd.github.io

Personal website built with Quarto

genomeassembler

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

github-pages-intro

Lesson materials for creating a personal website with Github Pages

infant_gut_microbiome

Transposons in the infant gut microbiome analysis

kd-mendotawinter

Microbial community analysis of Lake Mendota during winter months for Kali Denis' undergraduate project

lake-mags

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

mapmetasvsrefs

Pipeline for mapping a bunch of metagenomes to a bunch of reference genomes with bbmap. Then calculating the average percent identity and coverage values for all.

mcfamodule

Teaching module on genome-resolved metagenomic binning

mehg

Exploring the phylogenetic and metabolic diversity of microbial mercury methylation

metabolishmm

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

metag-bin-analysis

micdiv

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

obscurepos

Genome-resolved metagenomics of photosynthetic EBPR

ppk1_database

Repository for assigning Accumulibacter clade designations based on ppk1 nomenclature

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

r3r4

Metagenomic assembly and metatranscriptomic analysis of co-occuring Accumulibacter populations

resources

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