mikemc / speedyseq
Speedy versions of phyloseq functions
☆46Updated 7 months ago
Related projects ⓘ
Alternatives and complementary repositories for speedyseq
- Miscellaneous functions for metagenomic analysis.☆46Updated 5 months ago
- Compare different differential abundance and expression methods☆50Updated 2 years ago
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆69Updated 2 years ago
- Functions for compositional analysis of high throughput sequencing☆29Updated 11 months ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- functions for analyzing phyloseq data☆26Updated 3 months ago
- The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures☆13Updated 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 last year
- A set of R scripts for the analysis of microbial profiles☆40Updated 6 months ago
- Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.☆27Updated 2 years ago
- Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files☆31Updated 7 years ago
- power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA☆35Updated 8 years ago
- An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…☆33Updated 4 years ago
- Tranform files to the microtable object in microeco package☆22Updated this week
- Fantaxtic - Nested Bar Plots for Phyloseq Data☆26Updated 4 months ago
- diversity estimation under ecological networks☆83Updated last year
- Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)☆18Updated 2 years ago
- The is mostly a wrapper tool using phyloseq and microbiome R packages.☆33Updated last year
- A robust and fast clustering method for amplicon-based studies☆31Updated last year
- ☆50Updated 3 weeks ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated 2 months ago
- A microbiome analysis toolkit for R☆21Updated last year
- Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…☆57Updated 2 years ago
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆34Updated 7 months ago
- ☆21Updated 4 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆31Updated 4 years ago
- Phylogenetic Organization of Metagenomic Signals (POMS)☆19Updated last year
- Schloss Lab Tools for Reproducible Microbiome Research 💩☆29Updated last year
- [deprecated] Please use ampvis2☆8Updated 7 years ago
- Materials for the STAMPS 2019 course at the MBL in Woods Hole, MA, USA☆35Updated 5 years ago