R toolkit for single cell genomics

R Interface to Python

🦄 Scientific journal and sci-fi themed color palettes for ggplot2

A grammar of graphics for comparative genomics

R toolkit for the analysis of single-cell chromatin data

R package for MetaboAnalyst

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

DAS Tool

A companion R package for the MicrobiomeAnalyst web server

Make Picrust2 Output Analysis and Visualization Easier

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

Count Regression for Correlated Observations with the Beta-binomial

diversity estimation under ecological networks

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Species richness with high diversity

Differential Count Data Analysis Toolbox

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

MaAsLin3: Microbiome Multivariate Association with Linear Models

R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data

R package for sparse canonical correlation analysis with mixed data types (continuous, binary, zero-truncated)

Phylogenetic Organization of Metagenomic Signals (POMS)

Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations

R package for computing alpha and beta contributional diversity metrics

Infers species direct association networks