Packages pages: Packages, [Assess](/assess.md), [Advisories](/advisories.md), [Licence library](/licences.md), [Checks](/checks.md), [Archived](/archived.md)

# Packages

Search: "view:Spatial view:MicroarrayData view:GraphAndNetwork release:3.4"

The search reads these keywords as filters. Other words are searched as written.

- `license:MIT`: the licence family, by its name or an old keyword such as GPL
- `downloads:>1000`: at least that many distinct IPs a month
- `view:Bayesian`: a biocViews term, up to three
- `category:software`: a Bioconductor category: software, annotation, experiment or workflows
- `maintainer:"Hadley Wickham"`: the packages a person maintains now. Alone, with no catalogue in the address, their page
- `owner:tidyverse`: packages developed in that GitHub account's repositories. Alone, with no catalogue in the address, its page
- `ai:claude`: packages whose repository shows signs of that AI coding tool, ai:any of any tool
- `ai-found:pr`: how a tool was found: file, ignore, pr or commits
- `ai-model:opus`: a model named in the credit lines of commits
- `repo:yes`: a source repository on record, or repo:no
- `since:2026-01-01`: the latest release on or after that day
- `letter:D`: names that start with that letter
- `release:3.22`: the packages of a Bioconductor release, or release:all for every package ever seen
- `status:removed`: Bioconductor packages removed after an earlier release, status:unreleased never in one
- `-checks:failing`: a minus before checks, license, view, maintainer, owner, ai, ai-model, letter, tests or category leaves those packages out, and before compiled, deadline or repo gives the other answer
- `in:bioc`: a catalogue: all, cran, bioc, archived, or datasets for Datasets' search
- `sort:downloads`: an order: name, downloads, updated, or relevance for words alone

Catalogue: Bioconductor.
- Bioconductor release: Release 3.4 (2016)
- biocViews term: Spatial
- biocViews term: MicroarrayData
- biocViews term: GraphAndNetwork
- Topic page: [Spatial](/topics/bioc/Spatial.md)
- Topic page: [MicroarrayData](/topics/bioc/MicroarrayData.md)
- Topic page: [GraphAndNetwork](/topics/bioc/GraphAndNetwork.md)

201 packages on Bioconductor tagged Spatial or MicroarrayData or GraphAndNetwork, most distinct IPs first.

To search, add ?q=WORDS. To pick a catalogue, add catalogue=all, catalogue=cran or catalogue=bioc. To order the list, add sort=name, category, published, downloads, dependencies and order=asc or order=desc. Filters for Bioconductor: status (In the current release or not), release (Bioconductor release), category (Category), view (biocViews term), min_downloads (Distinct IPs a month), letter (First letter), license (Licence family offered), repository (Source repository on GitHub known), published_since (Latest version published on or after), maintainer (Maintainer), owner (Repository owner on GitHub), ai (AI coding tool), ai_found (AI tool found as), ai_model (Model named in commits). view takes up to three terms joined by commas, and lists packages tagged with any of them. min_downloads takes any whole number. maintainer takes a person's whole name and owner a GitHub login. ai takes any or a tool's key, ai_found file, ignore, pr or commits, and ai_model a model family's key, with the values and counts the page offers. not_ before the name of letter, license, check, task_view, tests, maintainer, owner, ai, ai_model, category or view leaves those packages out, as in not_check=problems.

| Package | Maintainer | Category | Latest version | Distinct IPs a month (sorted, high to low) | Needs |
| --- | --- | --- | --- | ---: | ---: |
| [graph](/bioc/graph.md) graph: A package to handle graph data structures | Bioconductor Package Maintainer | software | 28 Apr 2026 | 25,655 | 7 |
| [GSEABase](/bioc/GSEABase.md) Gene set enrichment data structures and methods | Bioconductor Package Maintainer | software | 28 Apr 2026 | 13,344 | 46 |
| [Rgraphviz](/bioc/Rgraphviz.md) Provides plotting capabilities for R graph objects | Kasper Daniel Hansen | software | 28 Apr 2026 | 11,263 | 10 |
| [RBGL](/bioc/RBGL.md) An interface to the BOOST graph library | Bioconductor Package Maintainer | software | 28 Apr 2026 | 10,698 | 9 |
| [graphite](/bioc/graphite.md) GRAPH Interaction from pathway Topological Environment | Gabriele Sales | software | 28 Apr 2026 | 7,012 | 48 |
| [KEGGgraph](/bioc/KEGGgraph.md) KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor | Jitao David Zhang | software | 28 Apr 2026 | 6,807 | 14 |
| [pathview](/bioc/pathview.md) a tool set for pathway based data integration and visualization | Weijun Luo | software | 28 Apr 2026 | 5,706 | 50 |
| [GOstats](/bioc/GOstats.md) Tools for manipulating GO and microarrays | Bioconductor Package Maintainer | software | 28 Apr 2026 | 2,437 | 63 |
| [SPIA](/bioc/SPIA.md) Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations | Adi Laurentiu Tarca | software | 28 Apr 2026 | 1,839 | 15 |
| [RCy3](/bioc/RCy3.md) Functions to Access and Control Cytoscape | Jing Chen | software | 28 Apr 2026 | 1,822 | 49 |
| [minet](/bioc/minet.md) Mutual Information NETworks | Patrick E. Meyer | software | 28 Apr 2026 | 1,543 | 1 |
| [qpgraph](/bioc/qpgraph.md) Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data | Robert Castelo | software | 28 Apr 2026 | 1,495 | 81 |
| [EnrichmentBrowser](/bioc/EnrichmentBrowser.md) Seamless navigation through combined results of set-based and network-based enrichment analysis | Ludwig Geistlinger | software | 28 Apr 2026 | 1,432 | 92 |
| [RedeR](/bioc/RedeR.md) Interactive visualization and manipulation of nested networks | Mauro Castro | software | 14 Jul 2026 | 1,317 | 23 |
| [BioNet](/bioc/BioNet.md) Routines for the functional analysis of biological networks | Marcus Dittrich | software | 28 Apr 2026 | 1,262 | 50 |
| [affydata](/bioc/affydata.md) Affymetrix Data for Demonstration Purpose | Robert D Shear | experiment | 5 May 2026 | 1,244 | 12 |
| [GeneNetworkBuilder](/bioc/GeneNetworkBuilder.md) GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data | Jianhong Ou | software | 28 Apr 2026 | 1,216 | 69 |
| [rTRM](/bioc/rTRM.md) Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks | Diego Diez | software | 28 Apr 2026 | 1,117 | 47 |
| [keggorthology](/bioc/keggorthology.md) graph support for KO, KEGG Orthology | VJ Carey | software | 28 Apr 2026 | 1,110 | 45 |
| [pandaR](/bioc/pandaR.md) PANDA Algorithm | Joseph N. Paulson | software | 28 Apr 2026 | 1,093 | 37 |
| [EGSEA](/bioc/EGSEA.md) Ensemble of Gene Set Enrichment Analyses | Monther Alhamdoosh | software | 28 Apr 2026 | 1,092 | 192 |
| [goProfiles](/bioc/goProfiles.md) goProfiles: an R package for the statistical analysis of functional profiles | Alex Sanchez | software | 28 Apr 2026 | 1,065 | 47 |
| [bladderbatch](/bioc/bladderbatch.md) Bladder gene expression data illustrating batch effects | Jeffrey T. Leek | experiment | 5 May 2026 | 1,049 | 7 |
| [biocGraph](/bioc/biocGraph.md) Graph examples and use cases in Bioinformatics | Florian Hahne | software | 28 Apr 2026 | 1,035 | 51 |
| [TRONCO](/bioc/TRONCO.md) TRONCO, an R package for TRanslational ONCOlogy | Luca De Sano | software | 28 Apr 2026 | 1,025 | 47 |
| [GraphAT](/bioc/GraphAT.md) Graph Theoretic Association Tests | Thomas LaFramboise | software | 28 Apr 2026 | 1,023 | 21 |
| [RTN](/bioc/RTN.md) RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons | Mauro Castro | software | 28 Apr 2026 | 1,023 | 142 |
| [apComplex](/bioc/apComplex.md) Estimate protein complex membership using AP-MS protein data | Denise Scholtens | software | 28 Apr 2026 | 1,009 | 48 |
| [MetaboSignal](/bioc/MetaboSignal.md) MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways | Andrea Rodriguez-Martinez | software | 23 Jul 2026 | 985 | 205 |
| [DEsubs](/bioc/DEsubs.md) DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments | Aristidis G. Vrahatis | software | 28 Apr 2026 | 971 | 100 |

This page lists 1 to 30 of 201 packages. [Next](/packages.md?catalogue=bioc&release=3.4&view=Spatial%2CMicroarrayData%2CGraphAndNetwork&sort=downloads&page=2)

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