Package: Fancy 0.99.4

Wanxin Lai

Fancy: Frequency and Nonlinear Correlation Hybrid Network Inference

Infers microbial co-abundance networks by combining mutual information (via MRNET) and distance correlation into a single hybrid edge score. Bootstrap resampling provides frequency-based confidence, and a weighted scoring function ranks edges for downstream module analysis. Designed for metagenome-assembled genome (MAG) count tables.

Authors:Wanxin Lai [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Fancy/json (API)

# Install 'Fancy' in R:

install.packages('Fancy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wala-github/fancy/issues

Datasets:

fancy_tiny_clr - Tiny example CLR-transformed abundance table
fancy_tiny_counts - Tiny example count table
fancy_tiny_coverage - Tiny example covered-fraction table
fancy_tiny_metadata - Tiny example sample metadata
fancy_tiny_taxonomy - Tiny example GTDB taxonomy table

On BioConductor:Fancy-0.99.4(bioc 3.24)

networkinference network metagenomics microbiome statisticalmethod

4.65 score 216 downloads 16 exports 46 dependencies

Last updated from:6820258800. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	136
linux-devel	OK	195
source / vignettes	OK	923
linux-release	OK	178
macos-release	OK	136
macos-oldrel	OK	85
windows-devel	OK	88
windows-release	OK	81
windows-oldrel	OK	82
wasm-release	OK	123

Exports:bootstrap_networks clean_sample_names clr_normalize export_cytoscape fancy filter_mags find_optimal_k hybrid_score parse_count_tables parse_gtdb_taxonomy phyla_palette plot plot_k_elbow plot_network show threshold_edges

Dependencies:bayesm bit bit64 boot cli clipr compositions cpp11 crayon DEoptimR dplyr energy generics glue gsl hms infotheo knnmi lifecycle magrittr MASS minet pillar pkgconfig prettyunits progress purrr R6 Rcpp RcppArmadillo readr rlang robustbase snow snowfall stringi stringr tensorA tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

Fancy: Hybrid Network Inference for Microbiome Co-Abundance Analysis

Rendered fromFancy_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-06-29
Started: 2026-03-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Access FancyResult slots with '$'	$,FancyResult-method
Bootstrap network inference	bootstrap_networks
Clean sample names from TSV column headers	clean_sample_names
CLR-normalise a count table	clr_normalize
Export a fancy result for Cytoscape	export_cytoscape
Run the full Fancy hybrid network inference pipeline	fancy
Tiny example CLR-transformed abundance table	fancy_tiny_clr
Tiny example count table	fancy_tiny_counts
Tiny example covered-fraction table	fancy_tiny_coverage
Tiny example sample metadata	fancy_tiny_metadata
Tiny example GTDB taxonomy table	fancy_tiny_taxonomy
FancyResult: S4 container for Fancy pipeline output	FancyResult-class
Filter MAGs by coverage and prevalence	filter_mags
Find optimal k for the kNN MI estimator	find_optimal_k
Compute hybrid edge score	hybrid_score
Parse per-sample TSV files into combined MAG-by-sample matrices	parse_count_tables
Parse a GTDB-format taxonomy file	parse_gtdb_taxonomy
Assign colours to phyla	phyla_palette
Plot elbow curve for k selection	plot_k_elbow
Plot the co-abundance network	plot_network
Plot the hybrid score distribution of a FancyResult	plot,FancyResult,missing-method
Display a FancyResult	show,FancyResult-method
Threshold scored edges	threshold_edges