Code to run the shiny functions for the MASAME suite
☆28Feb 4, 2020Updated 6 years ago
Alternatives and similar repositories for masame
Users that are interested in masame are comparing it to the libraries listed below
Sorting:
- Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and …☆10Jun 19, 2019Updated 6 years ago
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆50Mar 6, 2024Updated last year
- ggplot-based plots for vegan☆119Updated this week
- ☆14Apr 4, 2023Updated 2 years ago
- Python package for common tasks in bioinformatic.☆12Sep 24, 2025Updated 5 months ago
- A spatially explicit trait- and individual-based microbial systems modelling framework☆14Jan 29, 2026Updated last month
- Informatic Sequence Classification Trees☆15Jan 23, 2026Updated last month
- Sketch phylogenetic trees and networks☆24Feb 5, 2026Updated 3 weeks 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 last week
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆15Jul 20, 2023Updated 2 years ago
- ☆18Dec 2, 2022Updated 3 years ago
- Rarefaction scripts☆17Jan 30, 2026Updated last month
- Example code from metagenomics book (https://www.gitbook.com/book/kyclark/metagenomics/details)☆18Feb 1, 2019Updated 7 years ago
- estimate trophic position using stable isotope data☆19Jun 26, 2024Updated last year
- Visualize microbiome data with black magic ggtree☆68Sep 3, 2020Updated 5 years ago
- Ying's tools for analysis, with particular focus on microbiome data☆41Jan 27, 2026Updated last month
- This is a read-only mirror of the CRAN R package repository. BiodiversityR — Package for Community Ecology and Suitability Analysis. Ho…☆18Oct 29, 2025Updated 4 months ago
- These are scripts that I use frequently in genome annotation projects. Some of them have evolved awkwardly so the code is difficult to fo…☆16Nov 20, 2017Updated 8 years ago
- Generate de novo taxonomy of full length 16S rRNA sequences directly from environmental samples☆20Nov 23, 2024Updated last year
- TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region☆22Dec 11, 2025Updated 2 months ago
- A data analysis web-app written in R Shiny.☆22May 6, 2019Updated 6 years ago
- Statistical Analysis of Metagenomic Profiles☆94Jan 26, 2026Updated last month
- Slides and code for the Stable Isotope Mixing Models course given by Andrew Parnell and Andrew Jackson☆29Mar 28, 2025Updated 11 months ago
- Assign taxonomic ranks based on evolutionary divergence.☆23Mar 28, 2022Updated 3 years ago
- ☆23Mar 2, 2019Updated 7 years ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Apr 1, 2025Updated 11 months ago
- ☆20Oct 27, 2023Updated 2 years ago
- Python programming workshop for bioinformatics☆10Jul 13, 2021Updated 4 years ago
- Vanilla regression methods for microbiome differential abundance analysis☆61Nov 3, 2020Updated 5 years ago
- ☆23Sep 27, 2019Updated 6 years ago
- Some useful python scripts for biologists☆32Nov 19, 2024Updated last year
- Create an Interactive Pivot Table with Data Analysis Tools☆28Dec 9, 2020Updated 5 years ago
- Command-line utility to color objects of a KEGG pathway with arbitrary colors☆34Jul 10, 2015Updated 10 years ago
- BIO9905MERG1 – Bioinformatics for Environmental Sequencing (DNA metabarcoding)☆11Apr 9, 2023Updated 2 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆34Oct 26, 2020Updated 5 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Dec 4, 2018Updated 7 years ago
- Reorients assembled microbial sequences☆133Aug 21, 2025Updated 6 months ago
- ALDEx_bioc is the working directory for updating bioconductor☆30May 1, 2025Updated 10 months ago