rotheconrad

00_Annotation_Pipeline

Annotation Pipeline for TrEMBL, UniProt, and KEGG

00_Contig_Synteny

Build Gene Arrow Plot for Contig Synteny Across Multiple Contigs

00_in-situ_GeneCoverage

Workflow to calculate ANIr and sequence coverage (depth and breadth) of genome(s) / MAG(s) from metagenomes by gene, intergenic region, contig, and whole genome.

00_Pangenome_Analysis

Pangenome Analysis Workflow with Prodigal and CD-HIT

bacterial_strain_definition

Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis

EggNog_Annotation_Plots

Create stack bar plots and perform chi2 tests from EggNog Mapper annotations file.

F100_Prok_Recombination

Repository for F100 method of prokaryote recombination analysis

HeatSeq

Cluster munitions for microbial genomic sequence data

KEGGDecoder-binder

metabolic heatmap

Kraken-Bracken-plot

Creates stacked bar plots from Kracken and Bracken output.

rotheconrad/KEGGDecoder-binder

metabolic heatmap

rotheconrad/bacterial_strain_definition

Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis

rotheconrad/00_Annotation_Pipeline

Annotation Pipeline for TrEMBL, UniProt, and KEGG

rotheconrad/00_in-situ_GeneCoverage

Workflow to calculate ANIr and sequence coverage (depth and breadth) of genome(s) / MAG(s) from metagenomes by gene, intergenic region, contig, and whole genome.

rotheconrad/00_Pangenome_Analysis

Pangenome Analysis Workflow with Prodigal and CD-HIT

rotheconrad/ROCkIn

Preparation pipeline for ROCkOut

rotheconrad/00_Contig_Synteny

Build Gene Arrow Plot for Contig Synteny Across Multiple Contigs

rotheconrad/HeatSeq

Cluster munitions for microbial genomic sequence data

rotheconrad/Salinibacter_ruber_01

Repository for the first part of the Salinibacter ruber study.

rotheconrad/EggNog_Annotation_Plots

Create stack bar plots and perform chi2 tests from EggNog Mapper annotations file.

rotheconrad/F100_Prok_Recombination

Repository for F100 method of prokaryote recombination analysis

rotheconrad/Kraken-Bracken-plot

Creates stacked bar plots from Kracken and Bracken output.

rotheconrad/00_GATech_6720Class_Lab05

Bioinformatics Lab 05 for 6720 Class at GA Tech

rotheconrad/00_Scripts_General

General Scripts for file manipulation

rotheconrad/BioData

All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

rotheconrad/03_Thesis_Data

Supplemental Data Files for my PhD Thesis

rotheconrad/Custom_SNP_Reference

This is the workflow we explored for the 20 Transcriptomes project in 2016 in the McDaniel Lab to create custom snp corrected reference genomes for each individual with the goal of improving genome guided transcriptome mapping efficiency using a combination of published tools and one pearl script of ours to reformat the naming of the final output final.

rotheconrad/Descriptive_Metagenome_GoM

Code and notes to support the manuscript

rotheconrad/genome_diversity_pipeline

rotheconrad/GoM

Custom code for the Gulf of Mexico Project

rotheconrad/Metagenomic_Population_Tracking

Tracking prokaryote populations across samples with short-read mapping, MAGs, and population threshold detection

rotheconrad/MicrobeAnnotator

Pipeline for metabolic annotation of microbial genomes

rotheconrad/ModSimPy

Text and supporting code for Modeling and Simulation in Python

rotheconrad/planets

Planetary information for familiarization with git & GitHub basics

rotheconrad/Population-Genome-Simulator

Simulates a population of genomes around an ANI distribution

rotheconrad/ROCker_Macrolide_Models

ROCker models for macrolide resistance genes

rotheconrad/scikit-learn

scikit-learn: machine learning in Python