Alternatives and similar repositories for microbiomeSeq

Users that are interested in microbiomeSeq 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
• lch14forever / microbiomeViz
  Visualize microbiome data with black magic ggtree
  ☆68Updated 5 years ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆52Updated 3 years ago
• FrederickHuangLin / ANCOMBC
  Differential abundance (DA) and correlation analyses for microbial absolute abundance data
  ☆124Updated 2 weeks ago
• ChiLiubio / file2meco
  Transform files to the microtable object with microeco package
  ☆28Updated last month
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆28Updated 7 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 6 months ago
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆68Updated 3 weeks ago
• microsud / Tools-Microbiome-Analysis
  A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
  ☆115Updated 2 years ago
• adw96 / DivNet
  diversity estimation under ecological networks
  ☆83Updated last month
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• ggloor / CoDaSeq
  Functions for compositional analysis of high throughput sequencing
  ☆29Updated last year
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• knightlab-analyses / reference-frames
  ☆20Updated 5 years ago
• waldronlab / lefser
  R implementation of the LEfSe method
  ☆59Updated 4 months ago
• danknights / sourcetracker
  ☆77Updated last year
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 9 months ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆77Updated last month
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆119Updated last month
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆47Updated 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
• vmikk / metagMisc
  Miscellaneous functions for metagenomic analysis.
  ☆51Updated this week
• ryanjw / co-occurrence
  R scripts for performing co-occurrence analyses
  ☆34Updated 10 years ago
• thomazbastiaanssen / Tjazi
  A microbiome analysis toolkit for R
  ☆24Updated 2 years ago
• yhwu / idemp
  Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files
  ☆32Updated 8 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 3 months 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 3 years ago
• microsud / microbiomeutilities
  The is mostly a wrapper tool using phyloseq and microbiome R packages.
  ☆33Updated 2 years ago
• bulksoil / BioProtocol
  Repo for a Microbiome Protocol
  ☆10Updated 7 years ago
• biobakery / melonnpan
  Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
  ☆38Updated last year