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microeco

INFRA · APIS
Velocity0.0

Microbial Community Ecology Data Analysis

github.com/chiliubio/microeco ↗

A microbiome analysis framework quietly grew a metabolomics half

microbiomemetabolomicsr-packagenetwork-analysisbioinformaticsclass-framework
◆Current state
microeco is a class-based R framework for microbial community data, organised as trans_* analysis objects layered over a microtable container. The 2.x line added trans_metab for metabolomics in 2.1.0, built pathway calculation, enrichment and network functions onto it in 2.2.0, and reached 2.3.0 with trans_niche and trans_phylo classes plus graphml export from the network module. Release notes are dense bullet lists where a handful of new classes sit among fifteen to twenty parameter fixes.
◆Where it's heading
The package expands by adding analysis classes rather than rewriting existing ones, and the 2.x series widened its scope from microbial community structure to paired omics. trans_metab was the pivot; niche and phylogenetic classes in 2.3.0 extend the original microbiome side in parallel. Alongside that, a long maintenance thread tracks upstream churn - linewidth replacing size for ggplot2 v4.0, igraph namespace changes, lifecycle deprecations - which accounts for most of the bullet volume in any given release.
◆Prediction
Expect further trans_* classes filling gaps around the metabolomics arm, since every 2.x release so far has introduced at least one new class alongside its fix list.

◆Recent moves

  1. 1mo ago

    Niche and phylogenetic analysis classes join the framework

    Adds trans_niche and trans_phylo, extending the microbiome side of the framework while the metabolomics arm matures separately, plus graphml export from trans_network. The remaining dozen items are parameter and namespace fixes across trans_diff, trans_env, trans_abund and trans_classifier.

    View source ↗
  2. 3mo ago

    Pathway calculation, enrichment and network functions build out trans_metab

    Fills in the metabolomics class introduced one release earlier with four pathway functions: calculation, enrichment, enrichment plotting and pathway networks. This is the follow-through that makes trans_metab usable rather than a container, and it mirrors how the microbiome classes were fleshed out.

    View source ↗
  3. 4mo ago

    trans_metab class brings metabolomics into a microbiome framework

    ⚡ SPARK

    The release that widened microeco past its original remit. Everything in 2.2.0 and much of what follows builds on the class created here, which is why the 2.x line reads as two parallel arcs rather than one.

    View source ↗
  4. 6mo ago

    Statistical functions gain direct visualization, plus a volcano plot

    The 2.0 marker release shortens the common path by letting several visualization functions run directly off the preceding statistical step, and adds plot_volcano to trans_diff. More vegan transformation methods land in trans_norm. A workflow-smoothing release rather than a structural one, despite the major version bump.

    View source ↗
  5. 9mo ago

    ggplot2 v4.0 compatibility pass plus network and normalization options

    Mostly a compatibility release ahead of ggplot2 v4.0, fixing theme and width handling across trans_abund and trans_venn. Real additions are narrow: a p-adjust return option in cal_network, the CSS_p parameter in trans_norm and a new functional-redundancy community function.

    View source ↗
  6. 1y ago

    Parameter renames and namespace fixes across the trans_ classes

    Housekeeping: a cal_method to method rename in trans_env, a default flipped in trans_diff, a get.edges namespace fix and label positioning tweaks. Nothing here changes what the framework can analyse.

    View source ↗