Stars
R's data.table package extends data.frame:
An R-focused pipeline toolkit for reproducibility and high-performance computing
An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
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. …
An R package implementing the UMAP dimensionality reduction method.
Manipulate CSV files on the command line using dplyr
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
A user-friendly, highly customizable R package for building horizon plots in ggplot2
missForest is a nonparametric, mixed-type imputation method for basically any type of data for the statistical software R.
Bayesian inference of ancestral dates on bacterial phylogenetic trees
Tools for visualising microbial community amplicon data
R package for extracting mutation signatures from a list of somatic mutations
GSimp is a Gibbs sampler-based missing value imputation approach
Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)
COnstraint-based Reconstruction and Analysis (COBRA) of metabolic networks in R
R package for distilling functional annotations of bacterial genomes and metagenomes
Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
Three-Dimensional Tic-Tac-Toe! (To be played with another person.)
Supporting data for the DeepMicrobes paper
The goal of CSCpromoters is to extract, export and plot sequences of promoter regions from the genome fasta files.
Agent-based metabolic modelling of microbial communities in time and continuous µ-meter-scale space