zoecastillo / microbiomeExplorerLinks
The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.
☆72Updated 3 years ago
Alternatives and similar repositories for microbiomeExplorer
Users that are interested in microbiomeExplorer are comparing it to the libraries listed below
Sorting:
- Compare different differential abundance and expression methods☆52Updated 3 years ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated 3 months ago
- Speedy versions of phyloseq functions☆48Updated last year
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆32Updated 4 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 2 months ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆71Updated last year
- A set of R scripts for the analysis of microbial profiles☆41Updated last year
- ☆78Updated last year
- R implementation of the LEfSe method☆59Updated 5 months ago
- Functions for compositional analysis of high throughput sequencing☆29Updated last year
- Transform files to the microtable object with microeco package☆28Updated last month
- Visualize microbiome data with black magic ggtree☆68Updated 5 years ago
- Statistical analysis for sparse high-throughput sequencing☆69Updated 9 months ago
- SourceTracker2☆80Updated last year
- MaAsLin3: Microbiome Multivariate Association with Linear Models☆47Updated last week
- functions for analyzing phyloseq data☆28Updated 8 months ago
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆49Updated last year
- Fantaxtic - Nested Bar Plots for Phyloseq Data☆32Updated last year
- ☆41Updated 7 years ago
- Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…☆62Updated 3 years ago
- An R package for microbial community analysis in an environmental context☆67Updated 5 years ago
- The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures☆15Updated 2 years ago
- SHallow shOtGUN profiler☆53Updated 3 years ago
- R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.☆120Updated 2 months ago
- Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.☆27Updated 3 years ago
- R scripts for performing co-occurrence analyses☆34Updated 10 years ago
- A microbiome analysis toolkit for R☆24Updated 2 years ago
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Updated 7 months ago
- Tools for visualising microbial community amplicon data☆69Updated last month
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆39Updated last year