Package: anansi 1.3.0
Thomaz Bastiaanssen
anansi: Annotation-Based Analysis of Specific Interactions
Studies including both microbiome and metabolomics data are becoming more common. Often, it would be helpful to integrate both datasets in order to see if they corroborate each others patterns. All vs all association is imprecise and likely to yield spurious associations. This package takes a knowledge-based approach to constrain association search space, only considering metabolite-function pairs that have been recorded in a pathway database. This package also provides a framework to assess differential association.
Authors:
anansi_1.3.0.tar.gz
anansi_1.3.0.zip(r-4.7)anansi_1.3.0.zip(r-4.6)anansi_1.3.0.zip(r-4.5)
anansi_1.3.0.tgz(r-4.6-any)anansi_1.3.0.tgz(r-4.5-any)
anansi_1.3.0.tar.gz(r-4.7-any)anansi_1.3.0.tar.gz(r-4.6-any)
anansi_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
anansi/json (API)
NEWS
| # Install 'anansi' in R: |
| install.packages('anansi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thomazbastiaanssen/anansi/issues
Pkgdown/docs site:https://thomazbastiaanssen.github.io
- ec2cpd - Use linking data from the KEGG database.
- ec2ko - Use linking data from the KEGG database.
- FMT_KOs - Snippet of the CLR-transformed inferred functional data from the FMT Aging study.
- FMT_metab - Snippet of the CLR-transformed hippocampal metabolomics data from the FMT Aging study.
- FMT_metadata - Snippet of the metadata from the FMT Aging study.
- krebs - Simplified snippet of the Krebs cycle
On BioConductor:anansi-1.3.0(bioc 3.24)anansi-1.2.0(bioc 3.23)
microbiomemetabolomicsregressionpathwayskegg
Last updated from:536c3f2c55. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 234 | ||
| linux-devel-x86_64 | WARNING | 436 | ||
| source / vignettes | OK | 319 | ||
| linux-release-x86_64 | WARNING | 391 | ||
| macos-release-arm64 | WARNING | 241 | ||
| macos-oldrel-arm64 | WARNING | 260 | ||
| windows-devel | WARNING | 384 | ||
| windows-release | WARNING | 334 | ||
| windows-oldrel | WARNING | 307 | ||
| wasm-release | OK | 190 |
Exports:anansiAnansiTaleAnansiWebasMAEasMultiFactorasTSEdictionarygetEdgeListgetFeaturePairsgetGraphkegg_linkkrebsDemoWeblinkBiobakeryMapmetadatametadata<-MultiFactorpairwiseApplyplotAnansirandomMultiFactorrandomWebtableXtableYunfactorweaveKEGGweaveWeb
Dependencies:abindapebase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelBiostringscachemclicodetoolscpp11crayonDelayedArraydigestdplyrfarverfastmapforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphIRangesisobandjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMultiAssayExperimentnlmepatchworkpillarpkgconfigpolyclippurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystemfontstibbletidygraphtidyrtidyselecttidytreetreeioTreeSummarizedExperimenttweenrutf8vctrsviridisviridisLitewithrXVectoryulab.utils
Getting started with anansi
Rendered fromanansi.Rmdusingknitr::rmarkdownon May 27 2026.Last update: 2025-10-10
Started: 2025-02-07
Adjacency matrices
Rendered fromadjacency_matrices.Rmdusingknitr::rmarkdownon May 27 2026.Last update: 2025-10-10
Started: 2025-03-04
Association testing
Rendered fromdifferential_associations.Rmdusingknitr::rmarkdownon May 27 2026.Last update: 2025-10-10
Started: 2025-02-07
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Coercion functions for anansi | anansi-coercion as.data.frame.anansi::AnansiWeb as.list.anansi::AnansiWeb as.list.anansi::MultiFactor as.MAE as.MultiAssayExperiment as.TreeSummarizedExperiment as.TSE asMAE asMultiAssayExperiment asTreeSummarizedExperiment asTSE |
| AnansiTale S7 container class. Not intended for general use. | AnansiTale AnansiTale-class |
| AnansiWeb S7 container class | AnansiWeb |
| Methods for AnansiWeb S7 container class | AnansiWeb-methods dim.anansi::AnansiWeb dimnames.anansi::AnansiWeb names.anansi::AnansiWeb show.anansi::AnansiWeb |
| Methods for pairwise operations on AnansiWeb objects | AnansiWeb-pairwise pairs.anansi::AnansiWeb pairs.AnansiWeb pairwiseApply.anansi::AnansiWeb pairwiseApply.AnansiWeb |
| Get dictionary | dictionary dictionary-generic |
| Use linking data from the KEGG database. | ec2cpd ec2ko kegg_link |
| Snippet of the CLR-transformed inferred functional data from the FMT Aging study. | FMT_KOs |
| Snippet of the CLR-transformed hippocampal metabolomics data from the FMT Aging study. | FMT_metab |
| Snippet of the metadata from the FMT Aging study. | FMT_metadata |
| Get a listof edges | getEdgeList |
| Get a list of all pairs of features | getFeaturePairs |
| Get a graph object. | getGraph getGraph.list |
| Simplified snippet of the Krebs cycle | krebs |
| make a link data.frame for biobakery mapping files input | linkBiobakeryMap |
| Get metadata. | metadata metadata,anansi::AnansiWeb-method |
| Set metadata. | metadata.set metadata<- metadata<-,anansi::AnansiWeb-method |
| MultiFactor S7 container class | asMultiFactor MultiFactor |
| Methods for MultiFactor S7 container class | getGraph.anansi::MultiFactor levels.anansi::MultiFactor MultiFactor-methods unfactor unfactor,anansi::MultiFactor-method |
| Apply a function on each pair of features | pairwiseApply pairwiseApply-generic |
| Dissociation plot | plotAnansi plotAnansi-generic plotAnansi-methods |
| Generate a random AnansiWeb or MultiFactor | krebsDemoWeb randomAnansi randomMultiFactor randomWeb |
| Get tableX | tableX tableX-generic |
| Get tableY | tableY tableY-generic |
| Weave an AnansiWeb object | weaveKEGG weaveWeb |
| Weave an AnansiWeb | weaveWeb-methods weaveWeb.character weaveWeb.formula weaveWeb.MultiAssayExperiment weaveWeb.SingleCellExperiment weaveWeb.TreeSumarizedExperiment |
