Lagkouvardos / Rhea
A set of R scripts for the analysis of microbial profiles
☆41Updated 7 months ago
Alternatives and similar repositories for Rhea:
Users that are interested in Rhea are comparing it to the libraries listed below
- Compare different differential abundance and expression methods☆50Updated 2 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆31Updated 4 years ago
- 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
- Speedy versions of phyloseq functions☆46Updated 8 months ago
- SHallow shOtGUN profiler☆54Updated 2 years ago
- ☆23Updated 6 years ago
- The is mostly a wrapper tool using phyloseq and microbiome R packages.☆34Updated 2 years ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated last week
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆53Updated 4 months ago
- ☆51Updated this week
- A robust and fast clustering method for amplicon-based studies☆31Updated last year
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated 5 months ago
- Fantaxtic - Nested Bar Plots for Phyloseq Data☆27Updated 6 months ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project☆11Updated 2 years ago
- Scripts and tutorials on how to assemble individual microbial genomes from metagenomes☆80Updated 8 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆63Updated last year
- Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.☆27Updated 2 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆43Updated 4 years ago
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆27Updated last year
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆50Updated 2 years ago
- Functions for compositional analysis of high throughput sequencing☆29Updated last year
- A microbiome analysis toolkit for R☆21Updated last year
- Schloss Lab Tools for Reproducible Microbiome Research 💩☆30Updated last year
- Transform files to the microtable object with microeco package☆24Updated last month
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Updated last year
- The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures☆14Updated 2 years ago
- Sparse Cooccurence Network Investigation for Compositional data☆24Updated 2 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated last year