shandley

hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

Microbiome-Analysis-Using-R

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

virus_isolate_sequencing

Miscellaneous scripts for handling Illumina sequencing of virus isolates.

decatomb

Viral contig analysis (hecatomb-lite)

HIV-Oral

Analysis of the oral bacterial microbiome by 16S amplicon analysis in HIV infected men

rotabiome

Code used to generate the results of the rotabiome study

bonsai

Bonsai: Fast, flexible taxonomic analysis and classification

CHIKV_16S_analysis

dotfiles

:wrench: .files, including ~/.macos — sensible hacker defaults for macOS

durban_16S_tutorial

github-slideshow

A robot powered training repository :robot:

handley-lab

Hepb_Virume_Study

human_volunteer_rotabiome

Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics.

liver_injury_sbr_16S

neurodegeneration_16S

R code associated with neurodegeneration study

viral_genome_sop

virion

The global virome in one network

WNV-antibiotics

West Nile Virus Infection in mice treated with vehicle or various antibiotics: https://www.ncbi.nlm.nih.gov/pubmed/29590614