Reverse Dependencies of biom-format

The following projects have a declared dependency on biom-format:

• AMON-bio — Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins formicrobes or between microbes and host with or without metabolomics data
• amptk — AMPtk: amplicon tool kit
• birdman — Framework for differential microbiome abundance using Bayesian inference
• calour — CALOUR: exploratory and interactive microbiome analyses based on heatmap
• CAMIViz — A collection of tools to visualize CAMI profiling outputs
• clark-biom — Create BIOM-format tables from CLARK abundance tables.
• DEICODE — Robust Aitchison compositional biplots from sparse count data
• gemelli — Robust Aitchison Tensor Decomposition for sparse count data
• gneiss — Compositional data analysis tools and visualizations
• graftm — GraftM is a pipeline used for identifying and classifying marker gene reads from metagenomic datasets
• kraken-biom — Create BIOM-format tables from Kraken output.
• lefse — LEfSe determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
• metagenomix — metagenomix is a pipeline of pipelines to conduct metagenomic analyses on Slurm/Torque
• MetaPhlAn — MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
• micone — The Microbial Co-occurrence Network Explorer
• psmpa-fungi — PSMPA-Fungi: Prediction of Fungal Secondary Metabolism Potential using Amplicans
• q2-thapbi-pict — Qiime2 plugin for THAPBI PICT.
• qurro — Visualizes differentially ranked features and log-ratios of their sample abundances
• redbiom — no summary
• rhapsody — Microbe-metabolite interactions through neural networks
• SCNIC — A tool for finding and summarizing modules of highly correlated observations in compositional data
• taxpasta — TAXonomic Profile Aggregation and STAndardisation
• woltka — versatile meta-omic data classifier
• Xclusion-criteria — Generate interactive, user-defined visualisations to helpdefining inclusion/exclusion criteria on a metadata table.