joey711

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

shiny-phyloseq

An interactive web application for demonstrating and using phyloseq.

biom

Development version of the biom package for R

biomformat

Biom file format support in R/Bioconductor, vers. 1.x (JSON) and 2.x (HDF5) https://bioconductor.org/packages/release/bioc/html/biomformat.html

phyloseq-demo

Extended demonstrations of the phyloseq package

dada2docker

Docker build instructions for DADA2 and related functionality

waste-not-supplemental

Supplemental Materials for the "Waste Not, Want Not..." Article in PLoS Computational Biology

phyloseq-extensions

Extensions for the phyloseq package for R

2018_ASM_Workshop

Case study tutorial on using R to analyze microbiome data prepared for the 2018 ASM General Meeting in Atlanta, GA.

biomformat-oldfork

This is deprecated. Please post issues at the BioC-synced joey711/biomformat

biomformat0

Support for the biom file format in R/Bioconductor, versions 1.x (JSON) as well as 2.x (HDF5)

dataviz

A book covering the fundamentals of data visualization.

phyloseq-article-2013

The complete source for reproducing our 2013 PLoS ONE article describing the phyloseq package

shiny-examples

apps_script

biom-format

The Biological Observation Matrix (BIOM) Format Project

d3

A JavaScript visualization library for HTML and SVG.

ggplot2

An implementation of the Grammar of Graphics in R

meditron

Meditron is a suite of open-source medical Large Language Models (LLMs).

MetaPathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information

navasetal

R markdown supplementary files for navas et al

NCT03893422

Data-sharing repository for Randomized Clinical Trial NCT03893422 conducted by Pendulum Therapeutics.

npSeq

Vanilla npSeq downloaded from http://www3.nd.edu/~jli9/research.html

oiLabs

Source files for OpenIntro Statistics labs

rCharts_d3_sankey

rCharts implementation of d3 sankey plugin

rocker-versioned

Run earlier versions of R using docker

shiny

shinyFiles

A shiny extension for server side file access

sigma

SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data