Alternatives and similar repositories for microbiomeExplorer

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

• 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.
  ☆54Updated 2 months ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆48Updated last year
• ChiLiubio / file2meco
  Transform files to the microtable object with microeco package
  ☆27Updated 2 weeks 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
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆68Updated last year
• danknights / sourcetracker
  ☆76Updated last year
• 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
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆77Updated last month
• lch14forever / microbiomeViz
  Visualize microbiome data with black magic ggtree
  ☆68Updated 4 years ago
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆28Updated 6 months ago
• thomazbastiaanssen / Tjazi
  A microbiome analysis toolkit for R
  ☆24Updated 2 years ago
• knights-lab / BugBase
  ☆41Updated 7 years ago
• caporaso-lab / sourcetracker2
  SourceTracker2
  ☆80Updated last year
• FrederickHuangLin / ANCOM-Code-Archive
  Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…
  ☆63Updated 3 years ago
• a-h-b / dadasnake
  Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
  ☆49Updated last year
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 8 months ago
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆117Updated 3 weeks ago
• cafferychen777 / MicrobiomeStat
  Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
  ☆44Updated this week
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆43Updated this week
• waldronlab / lefser
  R implementation of the LEfSe method
  ☆59Updated 4 months ago
• statdivlab / radEmu
  ☆56Updated 3 weeks ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆54Updated 3 years ago
• umerijaz / microbiomeSeq
  An R package for microbial community analysis in an environmental context
  ☆67Updated 4 years ago
• microsud / dysbiosisR
  The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
  ☆15Updated 2 years ago
• gmteunisse / fantaxtic
  Fantaxtic - Nested Bar Plots for Phyloseq Data
  ☆31Updated last year
• knightlab-analyses / reference-frames
  ☆20Updated 5 years ago
• microsud / Tools-Microbiome-Analysis
  A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
  ☆116Updated 2 years ago