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
• caporaso-lab / mockrobiota
  A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.
  ☆83Updated 6 years ago
• biocore / redbiom
  Sample search by metadata and features
  ☆47Updated 2 years ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆78Updated 6 months ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆71Updated last year
• husonlab / megan-ce
  MEGAN Community Edition
  ☆72Updated last year
• lch14forever / microbiomeViz
  Visualize microbiome data with black magic ggtree
  ☆68Updated 5 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
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆71Updated 2 months ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆25Updated last year
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆106Updated 11 months ago
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆123Updated last year
• microgenomics / tutorials
  In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…
  ☆84Updated 7 years ago
• scwatts / fastspar
  Rapid and scalable correlation estimation for compositional data
  ☆97Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆61Updated last year
• biocore / songbird
  Vanilla regression methods for microbiome differential abundance analysis
  ☆60Updated 5 years ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆52Updated 3 years ago
• katholt / plotTree
  ☆68Updated 9 years ago
• biobakery / melonnpan
  Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
  ☆42Updated last year
• drostlab / orthologr
  Genome wide orthology inference and dNdS estimation
  ☆96Updated 4 months ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆81Updated 2 years ago
• umerijaz / microbiomeSeq
  An R package for microbial community analysis in an environmental context
  ☆67Updated 5 years ago
• ggloor / q2-aldex2
  qiime2 plugin for aldex2 for differential abundance analysis
  ☆11Updated 5 years ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated 3 weeks ago
• roblanf / sangeranalyseR
  functions to analyse sanger sequencing reads in R
  ☆104Updated 2 months ago
• microsud / Tools-Microbiome-Analysis
  A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
  ☆117Updated 2 years ago
• merenlab / illumina-utils
  A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
  ☆94Updated 2 months ago
• donovan-h-parks / STAMP
  Statistical Analysis of Metagenomic Profiles
  ☆94Updated last week
• waldronlab / curatedMetagenomicData
  Curated Metagenomic Data of the Human Microbiome
  ☆150Updated last week