jolespin / compositionalLinks
Python package for compositional data analysis including CLR/ILR, proportionality, partial correlation with basis shrinkage, and visualizations.
☆19Updated last year
Alternatives and similar repositories for compositional
Users that are interested in compositional are comparing it to the libraries listed below
Sorting:
- ☆27Updated last year
- Raspir, the rare species identifier☆11Updated last year
- microbial association network clustering algorithm☆13Updated last year
- ALDEx_bioc is the working directory for updating bioconductor☆28Updated last month
- Lowest Common Ancestor from a SAM/BAM/CRAM alignment file☆9Updated 9 months ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Updated 3 years ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆31Updated 10 months ago
- Implementation of Krona to QIIME2☆16Updated last year
- De novo VIral Genome Annotator☆21Updated 8 months ago
- Code for simulations and analysis for "Latent Variable Modeling for the Microbiome."☆21Updated 5 years ago
- A snakemake workflow for metagenomic projects☆14Updated 2 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…☆21Updated last year
- Confirming specific taxonomic groups within your samples.☆19Updated 4 years ago
- Processing support for Greengenes2☆12Updated last year
- Haplotype-aware genome assembly toolkit☆29Updated 5 years ago
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Updated 4 years ago
- Maximum Likelihood Amplicon Pipeline☆22Updated last year
- A functional profiler for metagenomes using FracMinHash☆16Updated 3 months ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 3 years ago
- COmpositional Zero-Inflated Network Estimation☆10Updated last year
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)☆17Updated 2 months ago
- Factorize metagenotypes to infer strains and their abundances☆12Updated 8 months ago
- Advanced metagenomic Sequence Analysis in R☆15Updated 6 years ago
- Bioinformatics pipeline for nanopore sequencing data☆11Updated 6 years ago
- mSWEEP High-resolution sweep metagenomics using fast probabilistic inference☆14Updated 7 months ago
- C++ tools for NCBI taxonomy tasks☆11Updated 3 years ago
- A repo to reproduce the experiments in the YACHT manuscript☆11Updated last year
- ☆36Updated last year