Alternatives and similar repositories for SHOGUN

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

• edamame-course / Metagenome
  ☆23Updated 6 years ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 5 months ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆24Updated 7 months ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 4 months ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 4 years ago
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆31Updated last month
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆59Updated 9 months ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• statdivlab / radEmu
  ☆55Updated 2 weeks ago
• ctmrbio / stag-mwc
  StaG Metagenomic Workflow Collaboration
  ☆29Updated 9 months ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆54Updated 3 years ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated last year
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆53Updated 10 months ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• thomazbastiaanssen / Tjazi
  A microbiome analysis toolkit for R
  ☆22Updated last year
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆81Updated 9 years ago
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆48Updated last year
• EnvGen / metagenomics-workshop
  Metagenomics Workshop
  ☆28Updated 8 years ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated last year
• 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…
  ☆36Updated 2 months ago
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆35Updated last week
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated last year
• CAMI-challenge / OPAL
  OPAL: Open-community Profiling Assessment tooL
  ☆28Updated 4 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…
  ☆71Updated 2 years ago