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amon

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data

ampvis2

Tools for visualising amplicon data

asm-2024

Nephele at ASM Microbe 2024

biom-format

The Biological Observation Matrix (BIOM) Format Project

biomformat

bpexploder

Exploding Boxplots HTML Widget

breakaway

Species richness with high diversity

chorddiag

R interface to D3 chord diagrams

circosjs

R htmlwidget for the circosJS JavaScript library

cookie-autodelete

Firefox and Chrome WebExtension that deletes cookies and other browsing site data as soon as the tab closes, domain changes, browser restarts, or a combination of those events.

d3heatmap

A D3.js-based heatmap htmlwidget for R

docopts

Shell interpreter for docopt, the command-line interface description language.

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

fastx_toolkit

FASTA/FASTQ pre-processing programs

ggbiplot

A biplot based on ggplot2

ggiraph

make 'ggplot' graphics interactive

ggrepel

:round_pushpin: Repel overlapping text labels away from each other.

gitworkshop

A repository for GitHub class

highcharter

R wrapper for highcharts based on htmlwidgets

homebrew-self

edited homebrew formulae

krona

Interactively explore metagenomes and more from a web browser.

lemon

🍋 Lemon --- Freshing up your ggplots

lmertestr

Repository for the R-package lmerTest

maaslin

metaerg

micca

micca - MICrobial Community Analysis

minpath

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

networkd3

D3 JavaScript Network Graphs from R

nmf

NMF: A Flexible R package for Nonnegative Matrix Factorization