Alternatives and similar repositories for CoDaSeq

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

• ggloor / CoDa_microbiome_tutorial

  View on GitHub
  Workshop for NGS'18 conference, Barcelona 2018
  ☆24Nov 22, 2018Updated 7 years ago
• lmward / MetaPOAP

  View on GitHub
  the Metagenomic test for Presence Or Absence of Pathways
  ☆13Mar 4, 2019Updated 6 years ago
• hallucigenia-sparsa / seqtime

  View on GitHub
  The seqtime R package provides functions to analyse sequencing data time series and to simulate community dynamics
  ☆21Dec 9, 2022Updated 3 years ago
• ggloor / miseq_bin

  View on GitHub
  Standard tools and protocols for MiSeq amplicon sequencing of 16S rRNA genes
  ☆10Nov 14, 2022Updated 3 years ago
• knightlab-analyses / reference-frames

  View on GitHub
  ☆20Jun 8, 2020Updated 5 years ago
• Gibbons-Lab / mbtools

  View on GitHub
  R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
  ☆24Jan 24, 2024Updated 2 years ago
• borenstein-lab / MUSiCC

  View on GitHub
  MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
  ☆16Nov 7, 2019Updated 6 years ago
• statdivlab / tinyvamp

  View on GitHub
  ☆19Jul 17, 2023Updated 2 years ago
• wwood / OrfM

  View on GitHub
  simple and not slow ORF caller
  ☆21Nov 6, 2025Updated 3 months ago
• biocore / DEICODE

  View on GitHub
  Robust Aitchison PCA from sparse count data
  ☆37Aug 17, 2022Updated 3 years ago
• leylabmpi / Struo2

  View on GitHub
  Scalable creating/updating of metagenome profiling databases
  ☆62Jun 25, 2025Updated 7 months ago
• nsgrantham / mimix

  View on GitHub
  MIMIX: a Bayesian Mixed-Effects Model for Microbiome Data from Designed Experiments
  ☆11Jul 9, 2020Updated 5 years ago
• omixer / omixer-rpmR

  View on GitHub
  An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
  ☆12Dec 16, 2022Updated 3 years ago
• tbrowne5 / crisprHAL

  View on GitHub
  Generalizable Cas9/sgRNA prediction models for multiple Cas9 variants
  ☆10Jan 17, 2026Updated 3 weeks ago
• KarstensLab / microshades

  View on GitHub
  This repo contains the R microshades package, which contains a color blind accessible color palette with 30 unique colors and functions f…
  ☆70Jun 6, 2024Updated last year
• ewissel / hAMRoaster

  View on GitHub
  hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
  ☆22Mar 8, 2024Updated last year
• nick-youngblut / traitar3

  View on GitHub
  From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)
  ☆21Jul 8, 2024Updated last year
• AllTheBacteria / Phylign

  View on GitHub
  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…
  ☆12May 22, 2024Updated last year
• liaoherui / StrainScan

  View on GitHub
  High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
  ☆43Apr 8, 2024Updated last year
• Gibbons-Lab / scfa_predictions

  View on GitHub
  Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
  ☆10Jun 25, 2024Updated last year
• oharar / PointedSDMs

  View on GitHub
  ☆13Jul 6, 2022Updated 3 years ago
• MatthewRalston / kmerdb

  View on GitHub
  Python CLI for alignment-free genomics.
  ☆12Jan 8, 2026Updated last month
• ggloor / ALDEx2_dev

  View on GitHub
  ALDEx tool to examine compositional high-throughput sequence data with Welch's t-test
  ☆13Mar 7, 2019Updated 6 years ago
• edgraham / GhostKoalaParser

  View on GitHub
  Parser for Ghost Koala
  ☆10Aug 23, 2018Updated 7 years ago
• vuongle2 / BiomeNED

  View on GitHub
  BiomeNED main code
  ☆12Jul 25, 2019Updated 6 years ago
• caporaso-lab / cual-id

  View on GitHub
  A package for creating and managing sample identifiers in comparative -omics datasets.
  ☆23Jan 30, 2017Updated 9 years ago
• statdivlab / corncob

  View on GitHub
  Count Regression for Correlated Observations with the Beta-binomial
  ☆106Nov 13, 2025Updated 3 months ago
• R-Wright-1 / kraken_metaphlan_comparison

  View on GitHub
  R markdown documents copied from other folders on Dec 15th 2021
  ☆14Nov 4, 2025Updated 3 months ago
• lakarstens / ControllingContaminants16S

  View on GitHub
  ☆13Feb 6, 2020Updated 6 years ago
• stjudecloud / ngsderive

  View on GitHub
  Forensic analysis tool useful in backwards computing information from next-generation sequencing data.
  ☆11Jan 20, 2026Updated 3 weeks ago
• JTFouquier / explana

  View on GitHub
  Workflow to generate interactive feature selection report for cross-sectional or longitudinal studies
  ☆12May 12, 2025Updated 9 months ago
• guokai8 / microbial

  View on GitHub
  Do microbiome analysis with dada2 and phyloseq object
  ☆14Oct 9, 2024Updated last year
• josephpetrone / RESCUE

  View on GitHub
  Resolving Species Level Classification Using Emu
  ☆14Jun 14, 2024Updated last year
• tyjo / clv

  View on GitHub
  Compositional Lotka-Volterra
  ☆16May 31, 2024Updated last year
• zdk123 / SpiecEasi

  View on GitHub
  Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
  ☆229Oct 29, 2025Updated 3 months ago
• biocore / gemelli

  View on GitHub
  Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TE…
  ☆85Nov 3, 2025Updated 3 months ago
• benjjneb / LRASManuscript

  View on GitHub
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆34Oct 26, 2020Updated 5 years ago
• indraniel / fqgrep

  View on GitHub
  An approximate sequence pattern matcher for FASTQ/FASTA files.
  ☆32Jan 22, 2016Updated 10 years ago
• BenBeresfordJones / MGBC

  View on GitHub
  The Mouse Gastrointestinal Bacteria Catalogue
  ☆16Apr 14, 2022Updated 3 years ago