https://github.com/shandley/hecatomb

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

snakemake viral-metagenomes virome

Last synced: 23 Mar 2025

https://github.com/shandley/microbiome-analysis-using-r

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

16s dada2 microbiome phyloseq teaching

Last synced: 23 Mar 2025

https://github.com/shandley/virus_isolate_sequencing

Miscellaneous scripts for handling Illumina sequencing of virus isolates.

Last synced: 23 Mar 2025

https://github.com/shandley/dada2-workflow

Generalized dada2 workflow. Refer to the wiki for help and troubleshooting.

16s 16s-rrna asv dada2 microbiome phyloseq

Last synced: 23 Mar 2025

https://github.com/shandley/decatomb

Viral contig analysis (hecatomb-lite)

metagenomics pathogen-discovery virome

Last synced: 23 Mar 2025

https://github.com/shandley/hiv-oral

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

Last synced: 23 Mar 2025

https://github.com/shandley/viromedata

A starndardized data structrue for encoding and manipulating virome data.

Last synced: 23 Mar 2025

https://github.com/shandley/neurodegeneration_16s

R code associated with neurodegeneration study

Last synced: 23 Mar 2025

https://github.com/shandley/ampliseqr

Comprehensive R package for optimized 16S sequencing analysis with hardware acceleration

Last synced: 23 Mar 2025

https://github.com/shandley/handley-lab

Last synced: 23 Mar 2025

https://github.com/shandley/viromepower

A package for virome study power analysis

Last synced: 23 Mar 2025

https://github.com/shandley/github-slideshow

A robot powered training repository :robot:

Last synced: 23 Mar 2025

https://github.com/shandley/viral_genome_sop

Last synced: 23 Mar 2025

https://github.com/shandley/wnv-antibiotics

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

alphavirus antibiotics microbiome

Last synced: 23 Mar 2025

https://github.com/shandley/phyloseq-meta-check

A Rmarkdown approach to checking and fixing sample names to make them mergeable into a phyloseq object.

Last synced: 23 Mar 2025

https://github.com/shandley/rotabiome

Code used to generate the results of the rotabiome study

Last synced: 23 Mar 2025

https://github.com/shandley/chikv_16s_analysis

Last synced: 23 Mar 2025

https://github.com/shandley/durban_16s_tutorial

Last synced: 23 Mar 2025

https://github.com/shandley/liver_injury_sbr_16s

Last synced: 23 Mar 2025

https://github.com/shandley/awesome-virome

A listing of software, tools and databases useful for virome analysis

Last synced: 23 Mar 2025

https://github.com/shandley/bash-workflow

Last synced: 31 Mar 2025

https://github.com/shandley/asvqc

An amplicon sequence variant (ASV) quality control package

Last synced: 23 Mar 2025

https://github.com/shandley/macos-bash-setup

instructions for configuring your macOS terminal to function more like a standard Unix/Linux environment

bash gnu homebrew macos terminal

Last synced: 10 Mar 2025

https://github.com/shandley/ggplateplus

Last synced: 23 Mar 2025

https://github.com/shandley/tldrai

Last synced: 23 Mar 2025

https://github.com/shandley/gg2-dada2

Some code to convert the GreenGenes2 database to dada2

Last synced: 23 Mar 2025

https://github.com/shandley/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.

dada2 microbiome phyloseq

Last synced: 23 Mar 2025

https://github.com/shandley/polyprotein-assembler

An workflow to assemble viral polyproteins from metagenomic data

Last synced: 23 Mar 2025