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
  ☆501Updated last month
• microbiome / microbiome
  microbiome R package
  ☆299Updated 5 months ago
• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆354Updated last month
• ChiLiubio / microeco
  An R package for data analysis in microbial community ecology
  ☆232Updated this week
• zdk123 / SpiecEasi
  Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
  ☆211Updated 2 weeks ago
• thackl / gggenomes
  A grammar of graphics for comparative genomics
  ☆680Updated 4 months ago
• jbisanz / qiime2R
  Import qiime2 artifacts to R
  ☆171Updated 5 months ago
• LangilleLab / microbiome_helper
  A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
  ☆446Updated 5 months ago
• wilkox / gggenes
  ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
  ☆549Updated 3 weeks ago
• kevinblighe / EnhancedVolcano
  Publication-ready volcano plots with enhanced colouring and labeling
  ☆430Updated 11 months ago
• taowenmicro / EasyMicrobiomeR
  Using R language in microbiome analysis
  ☆327Updated 2 years ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆390Updated last week
• yiluheihei / microbiomeMarker
  R package for microbiome biomarker discovery
  ☆183Updated 3 months ago
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,094Updated last month
• qiime2 / qiime2
  Source for the QIIME 2 Framework (Q2F).
  ☆505Updated 3 weeks ago
• YuLab-SMU / ggtree
  Visualization and annotation of phylogenetic trees
  ☆875Updated last month
• YinLiLin / CMplot
  📊 Circular and Rectangular Manhattan Plot
  ☆572Updated last month
• ropensci / biomartr
  Genomic Data Retrieval with R
  ☆222Updated 4 months ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆416Updated this week
• stefpeschel / NetCoMi
  Network construction, analysis, and comparison for microbial compositional data
  ☆167Updated 2 months ago
• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆463Updated last month
• raivokolde / pheatmap
  Pretty heatmaps
  ☆257Updated last year
• YongxinLiu / EasyAmplicon
  Easy Amplicon data analysis pipeline
  ☆295Updated last month
• alserglab / fgsea
  Fast Gene Set Enrichment Analysis
  ☆401Updated 2 weeks ago
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆314Updated last week
• YuLab-SMU / MicrobiotaProcess
  A comprehensive R package for deep mining microbiome
  ☆188Updated last month
• mothur / mothur
  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…
  ☆272Updated last week
• cafferychen777 / ggpicrust2
  Make Picrust2 Output Analysis and Visualization Easier
  ☆135Updated this week
• hbctraining / Training-modules
  Materials for short, half-day workshops
  ☆329Updated this week
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆771Updated 7 months ago