A repository for large-scale microbiome datasets, formatted for phyloseq
☆41Apr 8, 2024Updated 2 years ago
Alternatives and similar repositories for MicrobeDS
Users that are interested in MicrobeDS are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A comprehensive and customizable R package for microbiome analysis.☆24Jun 12, 2026Updated last month
- METAgenomic LONgitudinal Differential Abundance method☆16Dec 17, 2019Updated 6 years ago
- ☆81Oct 16, 2024Updated last year
- Microbiome Analysis Plotting and Visualization☆12Jul 14, 2026Updated last week
- Speedy versions of phyloseq functions☆48Apr 21, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Import qiime2 artifacts to R☆183Dec 12, 2024Updated last year
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated last year
- Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data☆23May 16, 2026Updated 2 months ago
- The code for running the analysis component of CSI-Microbe☆11Jan 3, 2024Updated 2 years ago
- Assign genotypes to Salmonella Paratyphi A isolates using their whole-genome data.☆10Mar 6, 2025Updated last year
- A shiny package for microbiome functional enrichment analysis☆42Jul 1, 2026Updated 3 weeks ago
- R package for microbiome biomarker discovery☆200Feb 19, 2025Updated last year
- supplementary tables and files☆11Oct 13, 2023Updated 2 years ago
- Code for the identification step for CSI-Microbes☆31Nov 25, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆39Apr 9, 2026Updated 3 months ago
- The is mostly a wrapper tool using phyloseq and microbiome R packages.☆32Nov 23, 2022Updated 3 years ago
- microbiome R package☆318May 12, 2026Updated 2 months ago
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆17Mar 31, 2022Updated 4 years ago
- Statistical analysis for sparse high-throughput sequencing☆75Dec 17, 2024Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆28Feb 6, 2023Updated 3 years ago
- ☆13Feb 5, 2022Updated 4 years ago
- R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.☆25Jan 24, 2024Updated 2 years ago
- A Transcriptomics-Proteomics Integration Pipeline☆21Apr 11, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- scripts for microbiome analysis☆12Jul 25, 2024Updated 2 years ago
- R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.☆129Jun 1, 2026Updated last month
- A pan-cancer analysis of the microbiome in metastatic cancer (Battaglia et. al, Cell, 2024)☆16Apr 9, 2024Updated 2 years ago
- ☆19Dec 16, 2024Updated last year
- SHallow shOtGUN profiler☆52Mar 4, 2022Updated 4 years ago
- an R package to biotype a community☆14Oct 19, 2021Updated 4 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆43Sep 17, 2025Updated 10 months ago
- A Linear Discriminant Analysis Effect Size (LEfSe) wrapper.☆26Feb 2, 2017Updated 9 years ago
- Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat☆50Jun 6, 2026Updated last month
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A pipeline for the identification of fungi in public metagenomics datasets☆18Nov 23, 2020Updated 5 years ago
- 16S rRNA Sequencing Data from the Human Microbiome Project☆10May 14, 2026Updated 2 months ago
- Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination☆15Jun 17, 2026Updated last month
- Advanced metagenomic Sequence Analysis in R☆15Aug 17, 2018Updated 7 years ago
- The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures☆16Dec 2, 2022Updated 3 years ago
- accessory functions for processing microbial community data☆12Dec 24, 2022Updated 3 years ago
- ☆12Jun 12, 2019Updated 7 years ago