Alternatives and similar repositories for co-occurrence

Users that are interested in co-occurrence are comparing it to the libraries listed below

• microbiota / amplicon
  Statistics and visualization for amplicon data
  ☆71Updated 2 years ago
• caporaso-lab / sourcetracker2
  SourceTracker2
  ☆80Updated last year
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆72Updated 3 years ago
• Russel88 / MicEco
  Various functions for analysis of microbial community data
  ☆46Updated 3 weeks ago
• bulksoil / BioProtocol
  Repo for a Microbiome Protocol
  ☆10Updated 7 years ago
• danknights / sourcetracker
  ☆78Updated last year
• Linwei-Wu / Global-bacterial-diversity-in-WWTPs
  ☆23Updated 6 years ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆71Updated last year
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 5 years ago
• Mengting-Maggie-Yuan / warming-network-complexity-stability
  Computer code for the manuscript "Climate Warming Enhances Microbial Network Complexity and Stability"
  ☆50Updated 3 years ago
• umerijaz / microbiomeSeq
  An R package for microbial community analysis in an environmental context
  ☆67Updated 5 years ago
• moyn413 / nifHdada2
  dada2 formatted nifH database
  ☆12Updated last year
• microbma / earthnetwork
  Microbial co-occurrence network inferred from Earth Microbiome Project
  ☆26Updated 5 years ago
• lch14forever / microbiomeViz
  Visualize microbiome data with black magic ggtree
  ☆68Updated 5 years ago
• waldronlab / lefser
  R implementation of the LEfSe method
  ☆59Updated this week
• mahendra-mariadassou / phyloseq-extended
  Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…
  ☆33Updated 7 months ago
• mestaki / qiime2-to-BugBase
  ☆12Updated 4 years ago
• gmteunisse / fantaxtic
  Fantaxtic - Nested Bar Plots for Phyloseq Data
  ☆32Updated last year
• ChiLiubio / file2meco
  Transform files to the microtable object with microeco package
  ☆28Updated 2 months ago
• ggloor / CoDaSeq
  Functions for compositional analysis of high throughput sequencing
  ☆29Updated last year
• microsud / Tools-Microbiome-Analysis
  A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
  ☆115Updated 2 years ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆52Updated 3 years ago
• ChengGaoBerkeley / EPICON.Mycobiome
  ☆13Updated 4 years ago
• RiceMicrobiome / Edwards-et-al.-2014
  ☆14Updated 10 years ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• GuillemSalazar / EcolUtils
  Utilities for community ecology analysis
  ☆19Updated 5 years ago
• bacteria-archaea-traits / bacteria-archaea-traits
  A synthesis of bacterial and archaeal phenotypic trait data
  ☆35Updated last year
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆120Updated 2 months ago
• UMNFuN / FUNGuild
  FUNGuild: parsing OTUs into functional guilds
  ☆120Updated last year
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 4 months ago