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
  ☆70Updated 2 years ago
• danknights / sourcetracker
  ☆76Updated last year
• bulksoil / BioProtocol
  Repo for a Microbiome Protocol
  ☆10Updated 7 years ago
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆71Updated 2 years ago
• Russel88 / MicEco
  Various functions for analysis of microbial community data
  ☆45Updated 2 years ago
• caporaso-lab / sourcetracker2
  SourceTracker2
  ☆76Updated last year
• Linwei-Wu / Global-bacterial-diversity-in-WWTPs
  ☆23Updated 6 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• ChiLiubio / file2meco
  Transform files to the microtable object with microeco package
  ☆27Updated 3 months ago
• moyn413 / nifHdada2
  dada2 formatted nifH database
  ☆12Updated last year
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• umerijaz / microbiomeSeq
  An R package for microbial community analysis in an environmental context
  ☆67Updated 4 years ago
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• 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 4 months ago
• mestaki / qiime2-to-BugBase
  ☆12Updated 3 years ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆67Updated 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
• ggloor / CoDaSeq
  Functions for compositional analysis of high throughput sequencing
  ☆29Updated last year
• waldronlab / lefser
  R implementation of the LEfSe method
  ☆59Updated 2 months ago
• lch14forever / microbiomeViz
  Visualize microbiome data with black magic ggtree
  ☆68Updated 4 years ago
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆115Updated 3 months ago
• YongxinLiu / Zhang2018SCLS
  Rice (Oryza Sative) root microbiome time-course analysis. (Zhang2018SCLS)
  ☆32Updated 6 years ago
• knightlab-analyses / reference-frames
  ☆20Updated 5 years ago
• Mengting-Maggie-Yuan / warming-network-complexity-stability
  Computer code for the manuscript "Climate Warming Enhances Microbial Network Complexity and Stability"
  ☆48Updated 3 years ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆50Updated 3 years ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 6 months ago
• microbma / earthnetwork
  Microbial co-occurrence network inferred from Earth Microbiome Project
  ☆25Updated 5 years ago
• gmteunisse / fantaxtic
  Fantaxtic - Nested Bar Plots for Phyloseq Data
  ☆31Updated last year
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆54Updated last month
• donaldtmcknight / microDecon
  An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing
  ☆16Updated last year