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

# Packages

Search: "view:Spatial view:GeneRegulation release:3.18"

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 3.18 (2023)
- biocViews term: Spatial
- biocViews term: GeneRegulation
- Topic page: [Spatial](/topics/bioc/Spatial.md)
- Topic page: [GeneRegulation](/topics/bioc/GeneRegulation.md)

159 packages on Bioconductor tagged Spatial or GeneRegulation, 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 |
| --- | --- | --- | --- | ---: | ---: |
| [SpatialExperiment](/bioc/SpatialExperiment.md) S4 Class for Spatially Resolved -omics Data | Dario Righelli | software | 28 Apr 2026 | 10,718 | 64 |
| [TCGAbiolinks](/bioc/TCGAbiolinks.md) TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data | Tiago Chedraoui Silva | software | 28 Apr 2026 | 6,750 | 103 |
| [TFBSTools](/bioc/TFBSTools.md) Software Package for Transcription Factor Binding Site (TFBS) Analysis | Ge Tan | software | 28 Apr 2026 | 4,721 | 79 |
| [decoupleR](/bioc/decoupleR.md) decoupleR: Ensemble of computational methods to infer biological activities from omics data | Pau Badia-i-Mompel | software | 30 Oct 2025 | 3,634 | 41 |
| [Rsubread](/bioc/Rsubread.md) Mapping, quantification and variant analysis of sequencing data | Wei Shi | software | 28 Apr 2026 | 2,951 | 8 |
| [CNEr](/bioc/CNEr.md) CNE Detection and Visualization | Boris Lenhard | software | 28 Apr 2026 | 2,692 | 112 |
| [OmnipathR](/bioc/OmnipathR.md) OmniPath web service client and more | Denes Turei | software | 30 Apr 2026 | 2,685 | 89 |
| [DiffBind](/bioc/DiffBind.md) Differential Binding Analysis of ChIP-Seq Peak Data | Rory Stark | software | 21 Jul 2026 | 2,490 | 141 |
| [chromVAR](/bioc/chromVAR.md) Chromatin Variation Across Regions | Alicia Schep | software | 11 May 2026 | 2,255 | 134 |
| [universalmotif](/bioc/universalmotif.md) Import, Modify, and Export Motifs with R | Benjamin Jean-Marie Tremblay | software | 3 May 2026 | 2,133 | 39 |
| [viper](/bioc/viper.md) Virtual Inference of Protein-activity by Enriched Regulon analysis | Mariano J Alvarez | software | 28 Apr 2026 | 2,060 | 87 |
| [progeny](/bioc/progeny.md) Pathway RespOnsive GENes for activity inference from gene expression | Aurélien Dugourd | software | 28 Apr 2026 | 2,012 | 58 |
| [RcisTarget](/bioc/RcisTarget.md) RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions | Gert Hulselmans | software | no date on record | 1,724 |  |
| [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 |
| [GUIDEseq](/bioc/GUIDEseq.md) GUIDE-seq and PEtag-seq analysis pipeline | Lihua Julie Zhu | software | 28 Apr 2026 | 1,256 | 179 |
| [INSPEcT](/bioc/INSPEcT.md) Modeling RNA synthesis, processing and degradation with RNA-seq data | Stefano de Pretis | software | 28 Apr 2026 | 1,213 | 123 |
| [ATACseqQC](/bioc/ATACseqQC.md) ATAC-seq Quality Control | Jianhong Ou | software | 16 Jul 2026 | 1,150 | 172 |
| [ggspavis](/bioc/ggspavis.md) Visualization functions for spatial transcriptomics data | Lukas M. Weber | software | 16 Jul 2026 | 1,146 | 76 |
| [SPONGE](/bioc/SPONGE.md) Sparse Partial Correlations On Gene Expression | Markus List | software | 11 Jun 2026 | 1,143 | 187 |
| [BCRANK](/bioc/BCRANK.md) Predicting binding site consensus from ranked DNA sequences | Adam Ameur | software | 28 Apr 2026 | 1,138 | 15 |
| [NADfinder](/bioc/NADfinder.md) Call wide peaks for sequencing data | Jianhong Ou | software | 28 Apr 2026 | 1,122 | 225 |
| [rTRM](/bioc/rTRM.md) Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks | Diego Diez | software | 28 Apr 2026 | 1,117 | 47 |
| [SPOTlight](/bioc/SPOTlight.md) `SPOTlight`: Spatial Transcriptomics Deconvolution | Marc Elosua-Bayes | software | 28 Apr 2026 | 1,110 | 46 |
| [TFEA.ChIP](/bioc/TFEA.ChIP.md) TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment | Yosra Berrouayel | software | 28 Apr 2026 | 1,105 | 106 |
| [GDCRNATools](/bioc/GDCRNATools.md) GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC | Ruidong Li | software | 28 Apr 2026 | 1,097 | 235 |
| [pandaR](/bioc/pandaR.md) PANDA Algorithm | Joseph N. Paulson | software | 28 Apr 2026 | 1,093 | 37 |
| [cicero](/bioc/cicero.md) Predict cis-co-accessibility from single-cell chromatin accessibility data | Hannah Pliner | software | 28 Apr 2026 | 1,077 | 179 |
| [imcRtools](/bioc/imcRtools.md) Methods for imaging mass cytometry data analysis | Daniel Schulz | software | 19 May 2026 | 1,064 | 181 |
| [CAGEfightR](/bioc/CAGEfightR.md) Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor | Malte Thodberg | software | 28 Apr 2026 | 1,053 | 158 |
| [MoonlightR](/bioc/MoonlightR.md) Identify oncogenes and tumor suppressor genes from omics data | Matteo Tiberti | software | 28 Apr 2026 | 1,048 | 186 |

This page lists 1 to 30 of 159 packages. [Next](/packages.md?catalogue=bioc&release=3.18&view=Spatial%2CGeneRegulation&sort=downloads&page=2)

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R Observatory is independent of the R Project, CRAN and Bioconductor. The same page for people is at /packages?catalogue=bioc&release=3.18&view=Spatial%2CGeneRegulation, and every address is listed at /llms.txt.