mahendra-mariadassou / phyloseq-extendedLinks
Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul
☆33Updated 7 months ago
Alternatives and similar repositories for phyloseq-extended
Users that are interested in phyloseq-extended are comparing it to the libraries listed below
Sorting:
- Speedy versions of phyloseq functions☆48Updated last year
- Various functions for analysis of microbial community data☆46Updated 2 weeks ago
- 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
- Look Up Guild Information for Fungi in R☆22Updated 6 months ago
- functions for analyzing phyloseq data☆28Updated 8 months ago
- Miscellaneous functions for metagenomic analysis.☆51Updated last week
- A robust and fast clustering method for amplicon-based studies☆31Updated 2 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆71Updated last year
- Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files☆32Updated 8 years ago
- diversity estimation under ecological networks☆83Updated 2 months ago
- Tools for visualising microbial community amplicon data☆69Updated last month
- JAMP - Just Another Metabarcoding Pipeline☆37Updated 3 years ago
- An R package for microbial community analysis in an environmental context☆67Updated 5 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 2 months ago
- functions to analyse sanger sequencing reads in R☆102Updated 7 months ago
- Functions for compositional analysis of high throughput sequencing☆29Updated last year
- A set of R scripts for the analysis of microbial profiles☆41Updated last year
- Sequence Taxonomic Assignment by Massive Pairwise Alignments☆14Updated 2 years ago
- Compare different differential abundance and expression methods☆52Updated 3 years ago
- Species richness with high diversity☆67Updated 2 months ago
- Differential abundance (DA) and correlation analyses for microbial absolute abundance data☆125Updated last month
- ☆78Updated last year
- R scripts for performing co-occurrence analyses☆34Updated 10 years ago
- metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.☆16Updated 2 months ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆39Updated last year
- power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA☆39Updated 9 years 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
- Visualize microbiome data with black magic ggtree☆68Updated 5 years ago
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆163Updated last month
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆32Updated 4 years ago