Alternatives and similar repositories for PIDA

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

• giannamars / DEBmicroTrait.jl
  Genome-informed, trait-based dynamic energy budget modeling of microbes with ML analysis of emergent strategies
  ☆15Updated 3 weeks ago
• yoann-dufresne / SLIM
  A web app for environmental DNA metabarcoding analysis
  ☆11Updated 4 years ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆72Updated 2 years ago
• spxuw / DKI
  ☆39Updated 9 months ago
• meringlab / FlashWeave.jl
  Inference of microbial interaction networks from large-scale heterogeneous abundance data
  ☆90Updated 3 months ago
• umerijaz / microbiomeSeq
  An R package for microbial community analysis in an environmental context
  ☆67Updated 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
• ryanjw / co-occurrence
  R scripts for performing co-occurrence analyses
  ☆36Updated 11 years ago
• pr2database / pr2database
  Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
  ☆85Updated last month
• GuillemSalazar / EcolUtils
  Utilities for community ecology analysis
  ☆19Updated 5 years ago
• ramellose / CoNetinR
  Implementation of CoNet in R
  ☆16Updated 6 years ago
• bokulich-lab / RESCRIPt
  REference Sequence annotation and CuRatIon Pipeline
  ☆98Updated last week
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• danknights / sourcetracker
  ☆79Updated 2 years ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆78Updated 5 months ago
• Chang-Yu-Chang / ecoprospector
  Python package simulating artificial selection on microbial communities
  ☆14Updated 2 years ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆86Updated 3 years ago
• simon-ho / SydneyPhyloWorkshop
  Sydney Phylogenetics Workshop
  ☆68Updated 6 months ago
• Russel88 / MicEco
  Various functions for analysis of microbial community data
  ☆47Updated 3 months ago
• InaMariaDeutschmann / EnDED
  EnDED is a program that aims to detect environmentally-driven ("indirect") edges in an association network.
  ☆10Updated 2 years ago
• enormandeau / barque
  eDNA metabarcoding pipeline
  ☆42Updated 3 weeks ago
• ukaraoz / microtrait
  ☆44Updated last year
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆39Updated 2 years ago
• statdivlab / radEmu
  ☆61Updated 3 weeks ago
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆93Updated last month
• eukref / pipeline
  EukRef curation pipeline
  ☆13Updated 4 years ago
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆28Updated 11 months ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆25Updated last year
• mahendra-mariadassou / phyloseq-extended
  Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…
  ☆33Updated 2 months ago