Alternatives and similar repositories for docs:

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

• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆24Updated 4 months ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 3 months ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated 10 months ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆55Updated 6 months ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated 11 months ago
• microsud / microbiomeutilities
  The is mostly a wrapper tool using phyloseq and microbiome R packages.
  ☆34Updated 2 years ago
• edamame-course / Metagenome
  ☆23Updated 6 years ago
• ggloor / q2-aldex2
  qiime2 plugin for aldex2 for differential abundance analysis
  ☆10Updated 5 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆71Updated 2 years ago
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆31Updated 7 months ago
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆70Updated 2 years ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆46Updated 2 years ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 years ago
• biocore / DEICODE
  Robust Aitchison PCA from sparse count data
  ☆33Updated 2 years ago
• metageni / SUPER-FOCUS
  A tool for agile functional analysis of shotgun metagenomic data
  ☆24Updated 6 months ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆57Updated 5 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆54Updated 2 months ago
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆45Updated 8 months ago
• biocore / redbiom
  Sample search by metadata and features
  ☆47Updated last year
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆86Updated 5 months ago
• MadsAlbertsen / multi-metagenome
  Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
  ☆80Updated 8 years ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆73Updated last week
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated 11 months ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆64Updated last year
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆43Updated 4 years ago
• Microbial-Ecology-Group / AMRplusplus
  AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…
  ☆33Updated this week
• qiyunzhu / woltka
  Woltka: a versatile meta'omic data classifier
  ☆72Updated 5 months ago
• Finn-Lab / MGS-gut
  Analysing Metagenomic Species (MGS)
  ☆41Updated 4 years ago