Paul J. McMurdie's Projects
Case study tutorial on using R to analyze microbiome data prepared for the 2018 ASM General Meeting in Atlanta, GA.
Animation addon tool for phyloseq package
Development version of the biom package for R
The Biological Observation Matrix (BIOM) Format Project
Biom file format support in R/Bioconductor, vers. 1.x (JSON) and 2.x (HDF5) https://bioconductor.org/packages/release/bioc/html/biomformat.html
This is deprecated. Please post issues at the BioC-synced joey711/biomformat
Support for the biom file format in R/Bioconductor, versions 1.x (JSON) as well as 2.x (HDF5)
A JavaScript visualization library for HTML and SVG.
Docker build instructions for DADA2 and related functionality
A book covering the fundamentals of data visualization.
Tools to extract dendrogram plot data for use with ggplot
Make graph/network plots with the ggplot2 package for R
An implementation of the Grammar of Graphics in R
Quick introduction to ggplot2 (no knowledge of R assumed)
Official GitHub central page for joey711
Meditron is a suite of open-source medical Large Language Models (LLMs).
A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
R markdown supplementary files for navas et al
Data-sharing repository for Randomized Clinical Trial NCT03893422 conducted by Pendulum Therapeutics.
Vanilla npSeq downloaded from http://www3.nd.edu/~jli9/research.html
Source files for OpenIntro Statistics labs
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:
The complete source for reproducing our 2013 PLoS ONE article describing the phyloseq package
Extended demonstrations of the phyloseq package
Extensions for the phyloseq package for R
Experimental support for loading and interacting with QIIME files in R.
rCharts implementation of d3 sankey plugin
Bidirectional interface between SRI's Pathway Tools software and R