Alternatives and similar repositories for metagenomeSeq

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

• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• lch14forever / microbiomeViz
  Visualize microbiome data with black magic ggtree
  ☆68Updated 5 years ago
• edamame-course / Metagenome
  ☆23Updated 7 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 3 months ago
• scwatts / fastspar
  Rapid and scalable correlation estimation for compositional data
  ☆92Updated last year
• karkman / MetagenomeCourse2019
  Course material for the metagenomics course
  ☆44Updated 3 years ago
• 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
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆120Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆56Updated last year
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• rdpstaff / classifier
  RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
  ☆58Updated 2 years ago
• zifanzhu / MicroPro
  A microbial profiling framework for metagenomic analysis
  ☆24Updated 5 years ago
• victoriapascal / gutsmash
  gutSMASH
  ☆55Updated 8 months ago
• cafferychen777 / MicrobiomeStat
  Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
  ☆44Updated this week
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆55Updated 3 years ago
• waldronlab / lefser
  R implementation of the LEfSe method
  ☆59Updated 4 months ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆52Updated 3 years ago
• nearinj / Comparison_of_DA_microbiome_methods
  ☆56Updated last year
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• MVesuviusC / primerTree
  PrimerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs
  ☆52Updated this week
• EnvGen / metagenomics-workshop
  Metagenomics Workshop
  ☆28Updated 8 years ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆77Updated last month
• danknights / sourcetracker
  ☆77Updated last year
• biobakery / melonnpan
  Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
  ☆38Updated last year
• donovan-h-parks / STAMP
  Statistical Analysis of Metagenomic Profiles
  ☆93Updated 5 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…
  ☆63Updated 3 years ago
• segalab / SGVFinder
  ☆31Updated 2 years ago
• merenlab / illumina-utils
  A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
  ☆92Updated last year
• drostlab / orthologr
  Genome wide orthology inference and dNdS estimation
  ☆96Updated 2 weeks ago