Alternatives and similar repositories for phyloseq

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

• benjjneb / dada2
  Accurate sample inference from amplicon data with single nucleotide resolution
  ☆534Updated last month
• microbiome / microbiome
  microbiome R package
  ☆308Updated 5 months ago
• wilkox / gggenes
  ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
  ☆571Updated 2 weeks ago
• YuLab-SMU / ggtree
  Visualization and annotation of phylogenetic trees
  ☆913Updated 2 weeks ago
• thackl / gggenomes
  A grammar of graphics for comparative genomics
  ☆741Updated 2 months ago
• LangilleLab / microbiome_helper
  A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
  ☆456Updated last year
• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆377Updated 2 months ago
• YinLiLin / CMplot
  📊 Circular and Rectangular Manhattan Plot
  ☆615Updated 9 months ago
• cooplab / popgen-notes
  Population genetics notes
  ☆686Updated 2 years ago
• zdk123 / SpiecEasi
  Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
  ☆224Updated 2 months ago
• ChiLiubio / microeco
  An R package for data analysis in microbial community ecology
  ☆262Updated this week
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆441Updated last month
• kevinblighe / EnhancedVolcano
  Publication-ready volcano plots with enhanced colouring and labeling
  ☆449Updated last month
• rachis-org / rachis
  Source for the QIIME 2 Framework (Q2F).
  ☆527Updated this week
• jbisanz / qiime2R
  Import qiime2 artifacts to R
  ☆175Updated last year
• knausb / vcfR
  Tools to work with variant call format files
  ☆265Updated 3 months ago
• yiluheihei / microbiomeMarker
  R package for microbiome biomarker discovery
  ☆193Updated 11 months ago
• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆483Updated 6 months ago
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,155Updated last week
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆312Updated 7 months ago
• mothur / mothur
  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…
  ☆275Updated 2 weeks ago
• vegandevs / vegan
  R package for community ecologists: popular ordination methods, ecological null models & diversity analysis
  ☆512Updated last month
• taowenmicro / EasyMicrobiomeR
  Using R language in microbiome analysis
  ☆347Updated 2 years ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆442Updated this week
• hbctraining / Training-modules
  Materials for short, half-day workshops
  ☆343Updated last week
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆394Updated 2 years ago
• YongxinLiu / EasyAmplicon
  Easy Amplicon data analysis pipeline
  ☆340Updated 2 months ago
• shuojiao / Community-assembly-processes-and-species-coexistences-of-agricultural-soils-microbiome
  ☆21Updated 6 years ago
• compgenomr / book
  ☆382Updated last year
• xia-lab / MetaboAnalystR
  R package for MetaboAnalyst
  ☆372Updated last week