elizabethmcd

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

BLAST-DAGMan

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

EBPR-MAGs

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

elizabethmcd.github.io

Personal website built with Quarto

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

metabolisHMM

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

ppk1_Database

Repository for assigning Accumulibacter clade designations based on ppk1 nomenclature

R3R4

Metagenomic assembly and metatranscriptomic analysis of co-occuring Accumulibacter populations

elizabethmcd/metabolisHMM

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

elizabethmcd/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

elizabethmcd/elizabethmcd.github.io

Personal website built with Quarto

elizabethmcd/MEHG

Exploring the phylogenetic and metabolic diversity of microbial mercury methylation

elizabethmcd/R3R4

Metagenomic assembly and metatranscriptomic analysis of co-occuring Accumulibacter populations

elizabethmcd/EBPR-MAGs

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

elizabethmcd/ppk1_Database

Repository for assigning Accumulibacter clade designations based on ppk1 nomenclature

elizabethmcd/Abigail_EBPR_SBR

Microbial community analysis of a lab-scale SBR simulating EBPR

elizabethmcd/AcDiv

Microdiversity and population structure of Accumulibacter using genome-resolved metagenomics

elizabethmcd/arcadia-docker-builds

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

elizabethmcd/bacMAGmining

Mining bacterial MAGs for bioactive molecules

elizabethmcd/cv

Elizabeth McDaniel CV

elizabethmcd/fermentedfood_mags_curation

Curated publicly available genomic data of fermented foods + microbes

elizabethmcd/genomeassembler

elizabethmcd/infant_gut_microbiome

Transposons in the infant gut microbiome analysis

elizabethmcd/Lake-MAGs

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

elizabethmcd/metabolisHMM2

Exploring genome annotations and phylogenies with HMM markers.

elizabethmcd/MicDiv

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

elizabethmcd/obscurePOS

Genome-resolved metagenomics of photosynthetic EBPR

elizabethmcd/peptide-mining

Workflow for mining bioactive peptides from proteomes

elizabethmcd/peptigate

Peptigate ("peptide" + "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.

elizabethmcd/R-amplicons

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

elizabethmcd/R1PopDynamics

Population dynamics at multiple scales of resolution of engineered bioreactor ecosystems

elizabethmcd/resources

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

elizabethmcd/Sakinaw

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

elizabethmcd/SAOB

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

elizabethmcd/SmORFinder

A command line tool to identify and annotate small proteins in microbial sequencing datasets.

elizabethmcd/TbasCO

elizabethmcd/tfdA

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

elizabethmcd/uTR

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