SWittouck / tidyamplicons
Functions to manipulate and visualize microbial community data
☆12Updated last year
Alternatives and similar repositories for tidyamplicons:
Users that are interested in tidyamplicons are comparing it to the libraries listed below
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆22Updated 7 months ago
- Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs☆18Updated 3 years ago
- A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.☆16Updated 3 months ago
- ☆22Updated last year
- Phylogenetic Organization of Metagenomic Signals (POMS)☆19Updated 2 years ago
- Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and …☆10Updated 5 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 7 months ago
- ☆16Updated 2 months ago
- Plot microbiome time series in parallel☆25Updated last year
- A functional profiler for metagenomes using FracMinHash☆15Updated last week
- MAG Circularization Method☆33Updated 2 years ago
- CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data☆21Updated last week
- Classify metagenomic contigs as eukaryotic or prokaryotic☆32Updated 2 years ago
- Metagenomic Estimation of Dietary Intake and Content.☆17Updated 3 weeks ago
- Dadaist2 🟨 Highway to R☆13Updated last month
- ☆25Updated last year
- Interpretative standards for AMR genotypes☆18Updated 7 months ago
- Pipeline for metagenome and metatranscriptome joint assembly☆20Updated last year
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆13Updated 7 months ago
- Calculate assocations between genes and traits☆22Updated 3 months ago
- A Hierarchical Approach to Pangenomics Inference☆11Updated 10 months ago
- Metabolic scanning and annotation of Metagenomes☆10Updated 2 months ago
- ☆15Updated last year
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Updated 11 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated this week
- Working with the outputs of sourmash in R☆26Updated last year
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆18Updated this week
- Hydrocarbon biodegradation gene annotation☆15Updated 2 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago