Alternatives and similar repositories for CoDaSeq

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

• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆48Updated last year
• 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
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆52Updated 3 years ago
• knightlab-analyses / reference-frames
  ☆20Updated 5 years ago
• thomazbastiaanssen / Tjazi
  A microbiome analysis toolkit for R
  ☆24Updated 2 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 4 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
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆28Updated 8 months ago
• adw96 / DivNet
  diversity estimation under ecological networks
  ☆83Updated 3 months ago
• GraceYoon / SPRING
  Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data
  ☆24Updated 3 years ago
• a-h-b / dadasnake
  Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
  ☆49Updated last year
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆69Updated last week
• 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 5 years ago
• brendankelly / micropower
  power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA
  ☆39Updated 9 years ago
• 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…
  ☆62Updated 3 years ago
• McMahonLab / TaxAss
  16S taxonomy assignment using an ecosystem-specific database.
  ☆17Updated 2 years ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆77Updated 3 months ago
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• lakarstens / ControllingContaminants16S
  ☆13Updated 5 years ago
• FrederickHuangLin / ANCOMBC
  Differential abundance (DA) and correlation analyses for microbial absolute abundance data
  ☆126Updated last month
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 5 years ago
• nhanhocu / metamicrobiomeR
  An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…
  ☆34Updated 4 years ago
• caporaso-lab / sourcetracker2
  SourceTracker2
  ☆80Updated last year
• ChiLiubio / file2meco
  Transform files to the microtable object with microeco package
  ☆28Updated 2 months ago
• bacteria-archaea-traits / bacteria-archaea-traits
  A synthesis of bacterial and archaeal phenotypic trait data
  ☆35Updated last year
• daisybio / namco
  ☆11Updated 6 months ago
• microsud / dysbiosisR
  The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
  ☆15Updated 2 years ago
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆120Updated 2 months ago