Alternatives and similar repositories for phylosmith

Users that are interested in phylosmith are comparing it to the libraries listed below

• 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
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆77Updated 2 months ago
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆48Updated last year
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆52Updated 3 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 3 months 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 7 months ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• ggloor / CoDaSeq
  Functions for compositional analysis of high throughput sequencing
  ☆29Updated last year
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆69Updated last month
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆71Updated last year
• vmikk / metagMisc
  Miscellaneous functions for metagenomic analysis.
  ☆51Updated this week
• McMahonLab / TaxAss
  16S taxonomy assignment using an ecosystem-specific database.
  ☆17Updated 2 years ago
• adw96 / DivNet
  diversity estimation under ecological networks
  ☆83Updated 2 months ago
• umerijaz / microbiomeSeq
  An R package for microbial community analysis in an environmental context
  ☆67Updated 5 years ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• microsud / microbiomeutilities
  The is mostly a wrapper tool using phyloseq and microbiome R packages.
  ☆33Updated 2 years ago
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆38Updated last year
• thomazbastiaanssen / Tjazi
  A microbiome analysis toolkit for R
  ☆24Updated 2 years ago
• vmaffei / dada2_to_picrust
  Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)
  ☆19Updated 6 years ago
• bacteria-archaea-traits / bacteria-archaea-traits
  A synthesis of bacterial and archaeal phenotypic trait data
  ☆35Updated last year
• lakarstens / ControllingContaminants16S
  ☆13Updated 5 years ago
• DenefLab / MicrobeMiseq
  Set of useful functions and scripts for analyzing amplicon Miseq data.
  ☆18Updated 9 years ago
• Russel88 / MicEco
  Various functions for analysis of microbial community data
  ☆46Updated last week
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆120Updated 2 months ago
• a-h-b / dadasnake
  Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
  ☆49Updated last year
• statdivlab / radEmu
  ☆55Updated last month
• 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 3 years ago
• mahsa-mousavi / eDNAFlow
  ☆21Updated 2 years ago
• drostlab / orthologr
  Genome wide orthology inference and dNdS estimation
  ☆96Updated last month