Alternatives and similar repositories for phyloseq-extended

Users that are interested in phyloseq-extended are comparing it to the libraries listed below

• Russel88 / MicEco
  Various functions for analysis of microbial community data
  ☆44Updated 2 years ago
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆48Updated last year
• yhwu / idemp
  Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files
  ☆31Updated 7 years ago
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• brendanf / FUNGuildR
  Look Up Guild Information for Fungi in R
  ☆21Updated 2 months ago
• gmteunisse / fantaxtic
  Fantaxtic - Nested Bar Plots for Phyloseq Data
  ☆30Updated 10 months ago
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆27Updated 4 months 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
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆66Updated last year
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• vmikk / metagMisc
  Miscellaneous functions for metagenomic analysis.
  ☆50Updated last week
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 years ago
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆38Updated last year
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆67Updated last month
• ryanjw / co-occurrence
  R scripts for performing co-occurrence analyses
  ☆34Updated 10 years ago
• adw96 / DivNet
  diversity estimation under ecological networks
  ☆83Updated last month
• MadsAlbertsen / ampvis
  [deprecated] Please use ampvis2
  ☆8Updated 7 years ago
• shandley / Microbiome-Analysis-Using-R
  Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
  ☆27Updated 2 years ago
• frederic-mahe / stampa
  Sequence Taxonomic Assignment by Massive Pairwise Alignments
  ☆14Updated last year
• VascoElbrecht / JAMP
  JAMP - Just Another Metabarcoding Pipeline
  ☆35Updated 3 years ago
• GuillemSalazar / EcolUtils
  Utilities for community ecology analysis
  ☆18Updated 4 years ago
• danknights / sourcetracker
  ☆74Updated last year
• terrimporter / CO1Classifier
  This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequen…
  ☆32Updated 2 years ago
• brendankelly / micropower
  power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA
  ☆37Updated 9 years ago
• metabaRfactory / metabaR
  metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
  ☆15Updated 4 months ago
• umerijaz / microbiomeSeq
  An R package for microbial community analysis in an environmental context
  ☆67Updated 4 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 4 years ago
• statdivlab / radEmu
  ☆55Updated last week
• aomlomics / tourmaline
  Amplicon sequence processing workflow using QIIME 2 and Snakemake
  ☆47Updated last month
• moyn413 / nifHdada2
  dada2 formatted nifH database
  ☆11Updated last year