functions for analyzing phyloseq data
☆28Feb 4, 2025Updated last year
Alternatives and similar repositories for phylosmith
Users that are interested in phylosmith are comparing it to the libraries listed below
Sorting:
- statdivlab's teaching materials for STAMPS @ the MBL in 2019☆11Jul 28, 2019Updated 6 years ago
- This is a collection of scripts for analyzing mixed 16S/18S amplicon sequences using tools such as qiime2, DADA2, deblur, and bbtools☆36Feb 24, 2026Updated last week
- Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files☆32Jun 21, 2017Updated 8 years ago
- Miscellaneous functions for metagenomic analysis.☆53Feb 20, 2026Updated 2 weeks ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆34Oct 26, 2020Updated 5 years ago
- Species richness with high diversity☆68Aug 5, 2025Updated 7 months ago
- Materials for the STAMPS 2019 course at the MBL in Woods Hole, MA, USA☆35Nov 8, 2019Updated 6 years ago
- Set of useful functions and scripts for analyzing amplicon Miseq data.☆18Sep 27, 2016Updated 9 years ago
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Oct 29, 2025Updated 4 months ago
- R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.☆122Feb 27, 2026Updated last week
- A manuscript exploring the effects of taxonomic bias on microbiome differential-abundance analysis.☆12Oct 30, 2023Updated 2 years ago
- Linear Decomposition Model☆25Jun 16, 2023Updated 2 years ago
- An R package for microbial community analysis in an environmental context☆67Sep 23, 2020Updated 5 years ago
- ☆11Apr 5, 2021Updated 4 years ago
- Profiler for metagenomics based on NGLess☆13Feb 22, 2024Updated 2 years ago
- EukRef curation pipeline☆13May 11, 2021Updated 4 years ago
- accessory functions for processing microbial community data☆12Dec 24, 2022Updated 3 years ago
- Prediction of microbial interactions in complex communities☆11Aug 14, 2024Updated last year
- Transform files to the microtable object with microeco package☆28Feb 13, 2026Updated 3 weeks ago
- Various functions for analysis of microbial community data☆47Oct 1, 2025Updated 5 months ago
- ☆14Jun 26, 2025Updated 8 months ago
- diversity estimation under ecological networks☆83Jul 29, 2025Updated 7 months ago
- R Interfaces to Phylogenetic Software☆12Sep 15, 2025Updated 5 months ago
- Sequence Taxonomic Assignment by Massive Pairwise Alignments☆14Jun 27, 2023Updated 2 years ago
- ☆13Feb 6, 2020Updated 6 years ago
- Do microbiome analysis with dada2 and phyloseq object☆14Oct 9, 2024Updated last year
- Import qiime2 artifacts to R☆176Dec 12, 2024Updated last year
- Threshold Indicator Taxa Analysis☆16Oct 16, 2025Updated 4 months ago
- GRAbB (Genome Region Assembly by Baiting) is a program designed to assemble selected regions of the genome or transcriptome using referen…☆13Nov 6, 2020Updated 5 years ago
- The is mostly a wrapper tool using phyloseq and microbiome R packages.☆32Nov 23, 2022Updated 3 years ago
- STAMPS 2018 course☆15Aug 8, 2018Updated 7 years ago
- Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat☆47Feb 3, 2026Updated last month
- R package MiscMetabar: Miscellaneous functions for metabarcoding analysis☆19Feb 20, 2026Updated 2 weeks ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆39Nov 18, 2023Updated 2 years ago
- Look Up Guild Information for Fungi in R☆23Mar 20, 2025Updated 11 months ago
- Code, unit tests, and tutorials for running PICRUSt2☆381Nov 27, 2025Updated 3 months ago
- Protist Ribosomal Reference database (PR2) - SSU rRNA gene database☆85Feb 26, 2026Updated last week
- ☆19Feb 24, 2026Updated last week
- Workshop materials for the Second Benthic Invertebrates, Metagenomics, and Bioinformatics Workshop at the TAMUCC Harte Institute in Corpu…☆22Jan 19, 2018Updated 8 years ago