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bioawk

BWK awk modified for biological data

centrifuge

Classifier for metagenomic sequences

cppnumericalsolvers

a lightweight C++17 library of numerical optimization methods for nonlinear functions (Including L-BFGS-B for TensorFlow)

dashr

R package for Dirichlet adaptive shrinkage and smoothing

deepcoda

Deep learning for personalized interpretability for compositional health data

deltacomp

Functions to analyse compositional data and produce confidence intervals for relative increases and decreases in the compositional components

despawn

Code of DeSpaWN ((https://doi.org/10.1073/pnas.2106598119)

detect-nahr

detecting non-allelic homologous recombination from short-read data

hmipipeline

kernelknn

Kernel k Nearest Neighbors in R

lmcrcoda

Cellwise and rowwise robust linear regression with compositional covariates

microbiome-variable-selection

r-codacore

recipes

Pipeable steps for feature engineering and data preprocessing to prepare for modeling

robregcc

Robust regression with compositional covariates

selbal

selbal: selection of balances for microbial signatures

zinlda

R package for Zero-Inflated Latent Dirichlet Allocation

zir

Zero-Inflated (Wilcoxon and Kruskal–Wallis) Rank Test