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

# Packages

Search: "license:permissive view:VariantAnnotation view:Bayesian view:MicroarrayData"

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.
- biocViews term: VariantAnnotation
- biocViews term: Bayesian
- biocViews term: MicroarrayData
- Licence family offered: Permissive
- Topic page: [VariantAnnotation](/topics/bioc/VariantAnnotation.md)
- Topic page: [Bayesian](/topics/bioc/Bayesian.md)
- Topic page: [MicroarrayData](/topics/bioc/MicroarrayData.md)

102 packages on Bioconductor tagged VariantAnnotation or Bayesian or MicroarrayData, 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 |
| --- | --- | --- | --- | ---: | ---: |
| [VariantAnnotation](/bioc/VariantAnnotation.md) Annotation of Genetic Variants | Bioconductor Package Maintainer | software | 28 Apr 2026 | 9,771 | 76 |
| [maftools](/bioc/maftools.md) Summarize, Analyze and Visualize MAF Files | Anand Mayakonda | software | 28 Apr 2026 | 3,419 | 26 |
| [infercnv](/bioc/infercnv.md) Infer Copy Number Variation from Single-Cell RNA-Seq Data | Christophe Georgescu | software | 28 Apr 2026 | 2,517 | 194 |
| [celda](/bioc/celda.md) CEllular Latent Dirichlet Allocation | Joshua Campbell | software | 28 Apr 2026 | 2,011 | 127 |
| [sesameData](/bioc/sesameData.md) Supporting Data for SeSAMe Package | Wanding Zhou | experiment | 5 May 2026 | 1,198 | 72 |
| [PureCN](/bioc/PureCN.md) Copy number calling and SNV classification using targeted short read sequencing | Markus Riester | software | 28 Apr 2026 | 1,083 | 101 |
| [decontX](/bioc/decontX.md) Decontamination of single cell genomics data | Joshua Campbell | software | 28 Apr 2026 | 1,040 | 233 |
| [bladderbatch](/bioc/bladderbatch.md) Bladder gene expression data illustrating batch effects | Jeffrey T. Leek | experiment | 5 May 2026 | 949 | 7 |
| [CoGAPS](/bioc/CoGAPS.md) Coordinated Gene Activity in Pattern Sets | Elana J. Fertig | software | 28 Apr 2026 | 805 | 94 |
| [NormalyzerDE](/bioc/NormalyzerDE.md) Evaluation of normalization methods and calculation of differential expression analysis statistics | Jakob Willforss | software | 28 Apr 2026 | 797 | 106 |
| [phenopath](/bioc/phenopath.md) Genomic trajectories with heterogeneous genetic and environmental backgrounds | Kieran Campbell | software | 28 Apr 2026 | 785 | 54 |
| [ASSIGN](/bioc/ASSIGN.md) Adaptive Signature Selection and InteGratioN (ASSIGN) | Ying Shen | software | 28 Apr 2026 | 770 | 93 |
| [TVTB](/bioc/TVTB.md) TVTB: The VCF Tool Box | Kevin Rue-Albrecht | software | 28 Apr 2026 | 758 | 159 |
| [minfiData](/bioc/minfiData.md) Example data for the Illumina Methylation 450k array | Kasper Daniel Hansen | experiment | 5 May 2026 | 731 | 146 |
| [myvariant](/bioc/myvariant.md) Accesses MyVariant.info variant query and annotation services | Adam Mark, Chunlei Wu | software | 28 Apr 2026 | 701 | 123 |
| [AMARETTO](/bioc/AMARETTO.md) Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression | Olivier Gevaert | software | 28 Apr 2026 | 700 | 149 |
| [RJMCMCNucleosomes](/bioc/RJMCMCNucleosomes.md) Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq) | Astrid Deschênes | software | 28 Apr 2026 | 691 | 67 |
| [seqCAT](/bioc/seqCAT.md) High Throughput Sequencing Cell Authentication Toolkit | Erik Fasterius | software | 28 Apr 2026 | 680 | 99 |
| [cellbaseR](/bioc/cellbaseR.md) Querying annotation data from the high performance Cellbase web | Mohammed OE Abdallah | software | 28 Apr 2026 | 666 | 62 |
| [bandle](/bioc/bandle.md) An R package for the Bayesian analysis of differential subcellular localisation experiments | Oliver M. Crook | software | 29 Apr 2026 | 646 | 239 |
| [BaalChIP](/bioc/BaalChIP.md) BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes | Ines de Santiago | software | 29 Apr 2026 | 623 | 103 |
| [geneAttribution](/bioc/geneAttribution.md) Identification of candidate genes associated with genetic variation | Arthur Wuster | software | 28 Apr 2026 | 610 | 76 |
| [BUSseq](/bioc/BUSseq.md) Batch Effect Correction with Unknow Subtypes for scRNA-seq data | Fangda Song | software | 28 Apr 2026 | 600 | 31 |
| [gemma.R](/bioc/gemma.R.md) A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses | Paul Pavlidis | software | 5 Oct 2026 | 590 | 92 |
| [ipdDb](/bioc/ipdDb.md) IPD IMGT/HLA and IPD KIR database for Homo sapiens | Steffen Klasberg | software | 28 Apr 2026 | 574 | 65 |
| [IgGeneUsage](/bioc/IgGeneUsage.md) Differential gene usage in immune repertoires | Simo Kitanovski | software | 28 Apr 2026 | 573 | 79 |
| [CBNplot](/bioc/CBNplot.md) plot bayesian network inferred from gene expression data based on enrichment analysis results | Noriaki Sato | software | 28 Apr 2026 | 559 | 166 |
| [FlowSorted.Blood.450k](/bioc/FlowSorted.Blood.450k.md) Illumina HumanMethylation data on sorted blood cell populations | Andrew E Jaffe | experiment | 5 May 2026 | 522 | 144 |
| [BAGS](/bioc/BAGS.md) A Bayesian Approach for Geneset Selection | Alejandro Quiroz-Zarate | software | 30 Oct 2025 | 507 | 8 |
| [AlphaMissenseR](/bioc/AlphaMissenseR.md) Accessing AlphaMissense Data Resources in R | Martin Morgan | software | 10 Sep 2026 | 504 | 59 |

This page lists 1 to 30 of 102 packages. [Next](/packages.md?catalogue=bioc&view=VariantAnnotation%2CBayesian%2CMicroarrayData&license=permissive&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&license=permissive&view=VariantAnnotation%2CBayesian%2CMicroarrayData, and every address is listed at /llms.txt.