adijatj

hafeZ

A tool for identifying active prophage elements through read mapping

PropagAtE

Prophage Activity Estimator

multitable_review

Code to accompany "Multitable Methods for Microbiome Data Integration"

teddy_vir_bac_marker_gene

Scripts for reproducing TEDDY virome/bacteriome analyses and figures

UHGV

Unified Human Gut Virome Catalog

Cenote-Taker3

Discover and annotate the virome

metagenomicspractical

Hands-on workflow for learning metagenomics including DNA mapping, binning, QC and annotation. Answers and example code available in the branch 'example' or on the practical webpage:

ictv-mmseqs2-protein-database

IBS_virome

norbis-virome-tutorial

Tutorial files for NORBIS summer school

VIRGO

growthcurver

Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, and the carrying capacity) provide meaningful population-level information with straight-forward biological interpretation.

rotabiome

Code used to generate the results of the rotabiome study

OMA

Orchestrating Microbiome Analysis

RoVI

premessa

R package for pre-processing of mass and flow cytometry data

Global_HEU_immune_microbiome

data, analysis scripts, and output figures for manuscript: Innate immune responses and gut microbiomes distinguish HIV exposed from unexposed children in a population-specific manner

adolescent

A prospective longitudinal study of the vaginal microbiome in perimenarcheal girls

Rhea

A set of R scripts for the analysis of microbial profiles

SOVAP_Soil_dsRNA

Supporting code for manuscript: Soil dsRNA Viromics

serratus

Ultra-deep search for novel viruses

ilifu_user_training

uct-srst2

MLST using srst2, implemented in Nextflow

Tychus

SOVAP

The Soil Virome Analysis Pipeline (SOVAP) is designed to process, analyze, and annotate viromics and metagenomics data using cutting-edge tools, providing valuable insights into the virome and microbial communities found in complex environments, such as soil ecosystems.

VFCs

Code for de novo discovery of viral families in virome data

JMAG_JVD

This is a repository of the codes used in the Tomofuji et al (prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features associated with diets, populations, and diseases).

PIGC

The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.

FDP

"Strain detection and genetic diversity in Mediterranean marine microbial populations" Final Degree Project repository. Includes scripts and files created and used to perform the analyses mentioned in the project manuscript.

R_Intro_Winter_2023

Introduction to the R programming language for research scientists