schuyler-smith / phylosmithLinks
functions for analyzing phyloseq data
☆28Updated 5 months ago
Alternatives and similar repositories for phylosmith
Users that are interested in phylosmith are comparing it to the libraries listed below
Sorting:
- Speedy versions of phyloseq functions☆48Updated last year
- 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
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 4 months ago
- Compare different differential abundance and expression methods☆50Updated 3 years ago
- Functions for compositional analysis of high throughput sequencing☆29Updated last year
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆67Updated last year
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Updated 4 months ago
- Miscellaneous functions for metagenomic analysis.☆50Updated last month
- Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files☆31Updated 8 years ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆54Updated last month
- Tools for visualising microbial community amplicon data☆67Updated 3 months ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆32Updated 4 years ago
- diversity estimation under ecological networks☆84Updated 3 months ago
- A robust and fast clustering method for amplicon-based studies☆31Updated 2 years ago
- The is mostly a wrapper tool using phyloseq and microbiome R packages.☆34Updated 2 years ago
- ☆56Updated this week
- 16S taxonomy assignment using an ecosystem-specific database.☆17Updated 2 years ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- A set of R scripts for the analysis of microbial profiles☆41Updated last year
- A synthesis of bacterial and archaeal phenotypic trait data☆35Updated last year
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆49Updated last year
- An R package for microbial community analysis in an environmental context☆67Updated 4 years ago
- Various functions for analysis of microbial community data☆45Updated 2 years ago
- Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)☆19Updated 6 years ago
- ☆76Updated last year
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated 2 months ago
- A microbiome analysis toolkit for R☆23Updated last year
- ☆21Updated 2 years ago
- An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…☆34Updated 4 years ago
- R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.☆115Updated 3 months ago