reptalex/phylofactor external links

---

GitHub - View repository

GitHub.dev - Open in online code editor

Star history - Growth chart over time

deps.dev - Dependencies and security vulnerabilities

Gitingest - Export source code for LLM usage

Repomix - Export source code for LLM usage

uithub - Export source code for LLM usage

Close

reptalex/phylofactor

Readme badge preview -

If you own this repo, copy the snippet below and add it to your README.md

---

Copy

[![RelatedRepos](https://img.shields.io/badge/related-repos-yellow)](https://relatedrepos.com/gh/reptalex/phylofactor)

Close

reptalex / phylofactorView on GitHubMore

• External links
• Readme badge

☆28Feb 27, 2024Updated 2 years ago

Alternatives and similar repositories for phylofactor

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

• mikemc / differential-abundance-theory

  View on GitHub
  A manuscript exploring the effects of taxonomic bias on microbiome differential-abundance analysis.
  ☆12Oct 30, 2023Updated 2 years ago
• shihuang047 / age-prediction

  View on GitHub
  ☆22Nov 6, 2020Updated 5 years ago
• katrikorpela / mare

  View on GitHub
  Microbiota Analysis in R Easily
  ☆12Jul 14, 2022Updated 3 years ago
• donovan-h-parks / PhyloRank

  View on GitHub
  Assign taxonomic ranks based on evolutionary divergence.
  ☆23Updated this week
• ropensci / phylotaR

  View on GitHub
  An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
  ☆25Aug 1, 2025Updated 7 months ago
• knightlab-analyses / reference-frames

  View on GitHub
  ☆20Jun 8, 2020Updated 5 years ago
• biocore / tax2tree

  View on GitHub
  Automated taxonomy decoration onto a tree
  ☆17Mar 10, 2023Updated 2 years ago
• qiime2 / q2-fragment-insertion

  View on GitHub
  ☆14Jan 27, 2026Updated last month
• mikemc / speedyseq

  View on GitHub
  Speedy versions of phyloseq functions
  ☆48Apr 21, 2024Updated last year
• jbisanz / MicrobeR

  View on GitHub
  Handy tools for Microbiome analysis in R
  ☆18May 22, 2019Updated 6 years ago
• gerberlab / MDSINE2

  View on GitHub
  ☆33Jan 21, 2026Updated last month
• nhanhocu / metamicrobiomeR

  View on GitHub
  An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…
  ☆34Nov 12, 2020Updated 5 years ago
• statdivlab / tinyvamp

  View on GitHub
  ☆19Feb 24, 2026Updated last week
• meren / BLAST-filtering-pipeline

  View on GitHub
  A very simple BLAST filtering pipeline
  ☆19Mar 28, 2014Updated 11 years ago
• jsilve24 / fido

  View on GitHub
  Multinomial Logistic-Normal Models (really fast)
  ☆20Feb 26, 2025Updated last year
• EESI / microbiome_embeddings

  View on GitHub
  ☆10Feb 21, 2020Updated 6 years ago
• jsilve24 / stray

  View on GitHub
  Stray has been renamed fido, development continues at jsilve24/fido
  ☆23Jan 26, 2022Updated 4 years ago
• statdivlab / stamps2019

  View on GitHub
  statdivlab's teaching materials for STAMPS @ the MBL in 2019
  ☆11Jul 28, 2019Updated 6 years ago
• biobakery / homebrew-biobakery

  View on GitHub
  Biobakery formulae for the Homebrew package manager
  ☆11Sep 9, 2019Updated 6 years ago
• shahinrostami / chord

  View on GitHub
  Engaging visualisations, made easy.
  ☆14Aug 7, 2024Updated last year
• biocore / BIRDMAn

  View on GitHub
  Bayesian Inferential Regression for Differential Microbiome Analysis
  ☆24Dec 19, 2023Updated 2 years ago
• bacpop / CELEBRIMBOR

  View on GitHub
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆27Jul 22, 2024Updated last year
• LewisLabUCSD / CellFie

  View on GitHub
  An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.
  ☆15Oct 19, 2022Updated 3 years ago
• biobakery / SparseDOSSA2

  View on GitHub
  ☆13Dec 2, 2024Updated last year
• vuongle2 / BiomeNED

  View on GitHub
  BiomeNED main code
  ☆12Jul 25, 2019Updated 6 years ago
• katcoyte / MK-SpikeSeq

  View on GitHub
  Protocols, data and code associated with the MK-SpikeSeq method for quantifying the absolute abundances of microbiota samples
  ☆12May 19, 2021Updated 4 years ago
• pmenzel / taxonomy-tools

  View on GitHub
  C++ tools for NCBI taxonomy tasks
  ☆12Jun 26, 2025Updated 8 months ago
• duncanwadsworth / dmbvs

  View on GitHub
  Dirichlet-Multinomial Bayesian Variable Selection
  ☆14Jun 13, 2024Updated last year
• statdivlab / groves

  View on GitHub
  Tools for analyzing trees
  ☆13Apr 16, 2025Updated 10 months ago
• tensorly / viz

  View on GitHub
  Easy visualization and evaluation of matrix and tensor factorization models
  ☆17Jan 4, 2026Updated 2 months ago
• FrederickHuangLin / ANCOMBC

  View on GitHub
  Differential abundance (DA) and correlation analyses for microbial absolute abundance data
  ☆131Sep 5, 2025Updated 6 months ago
• thackl / treemmer-animate

  View on GitHub
  ☆13Mar 28, 2018Updated 7 years ago
• refresh-bio / clusty

  View on GitHub
  ☆15Jan 28, 2026Updated last month
• EvaYiwenWang / Managing_batch_effects

  View on GitHub
  ☆14Apr 4, 2023Updated 2 years ago
• JTFouquier / ghost-tree

  View on GitHub
  creating hybrid-gene phylogenetic trees for diversity analyses
  ☆30Aug 23, 2022Updated 3 years ago
• slimsuite / diploidocus

  View on GitHub
  Diploid genome assembly analysis tools
  ☆14Sep 19, 2024Updated last year
• nathanhaigh / amos

  View on GitHub
  A clone of the official AMOS git repo on sourceforge: https://sourceforge.net/projects/amos/
  ☆18Nov 15, 2012Updated 13 years ago
• krisrs1128 / microbiome_plvm

  View on GitHub
  Code for simulations and analysis for "Latent Variable Modeling for the Microbiome."
  ☆21Dec 30, 2019Updated 6 years ago
• jlugomar / longitudinal_microbiome_analysis_public

  View on GitHub
  ☆18Feb 19, 2021Updated 5 years ago