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# Packages

Search: "view:VariantAnnotation view:Bayesian view:ExpressionData release:2.12"

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 2.12 (2013)
- biocViews term: VariantAnnotation
- biocViews term: Bayesian
- biocViews term: ExpressionData
- Topic page: [VariantAnnotation](/topics/bioc/VariantAnnotation.md)
- Topic page: [Bayesian](/topics/bioc/Bayesian.md)
- Topic page: [ExpressionData](/topics/bioc/ExpressionData.md)

22 packages on Bioconductor tagged VariantAnnotation or Bayesian or ExpressionData, 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 |
| --- | --- | --- | --- | ---: | ---: |
| [limma](/bioc/limma.md) Linear Models for Microarray and Omics Data | Gordon Smyth | software | 10 Aug 2026 | 44,656 | 6 |
| [DESeq2](/bioc/DESeq2.md) Differential gene expression analysis based on the negative binomial distribution | Michael Love | software | 28 Apr 2026 | 31,845 | 54 |
| [edgeR](/bioc/edgeR.md) Empirical Analysis of Digital Gene Expression Data in R | Yunshun Chen | software | 19 Oct 2026 | 31,065 | 10 |
| [VariantAnnotation](/bioc/VariantAnnotation.md) Annotation of Genetic Variants | Bioconductor Package Maintainer | software | 28 Apr 2026 | 9,771 | 76 |
| [pcaMethods](/bioc/pcaMethods.md) A collection of PCA methods | Henning Redestig | software | 28 Apr 2026 | 7,214 | 10 |
| [Rsubread](/bioc/Rsubread.md) Mapping, quantification and variant analysis of sequencing data | Wei Shi | software | 28 Apr 2026 | 2,722 | 8 |
| [baySeq](/bioc/baySeq.md) Empirical Bayesian analysis of patterns of differential expression in count data | Samuel Granjeaud | software | 28 Apr 2026 | 1,168 | 20 |
| [puma](/bioc/puma.md) Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) | Xuejun Liu | software | 28 Apr 2026 | 1,033 | 55 |
| [affylmGUI](/bioc/affylmGUI.md) GUI for limma Package with Affymetrix Microarrays | Gordon Smyth | software | 28 Apr 2026 | 967 | 55 |
| [limmaGUI](/bioc/limmaGUI.md) GUI for limma Package With Two Color Microarrays | Gordon Smyth | software | 28 Apr 2026 | 905 | 11 |
| [tigre](/bioc/tigre.md) Transcription factor Inference through Gaussian process Reconstruction of Expression | Antti Honkela | software | 28 Apr 2026 | 822 | 50 |
| [CoGAPS](/bioc/CoGAPS.md) Coordinated Gene Activity in Pattern Sets | Elana J. Fertig | software | 28 Apr 2026 | 805 | 94 |
| [EBcoexpress](/bioc/EBcoexpress.md) EBcoexpress for Differential Co-Expression Analysis | John A. Dawson | software | 28 Apr 2026 | 729 | 15 |
| [ternarynet](/bioc/ternarynet.md) Ternary Network Estimation | McCall N. Matthew | software | 28 Apr 2026 | 583 | 26 |
| [GRENITS](/bioc/GRENITS.md) Gene Regulatory Network Inference Using Time Series | Edward Morrissey | software | 28 Apr 2026 | 531 | 31 |
| [BitSeq](/bioc/BitSeq.md) Transcript expression inference and differential expression analysis for RNA-seq data |  |  | no date on record | 426 |  |
| [ensemblVEP](/bioc/ensemblVEP.md) R Interface to Ensembl Variant Effect Predictor |  |  | no date on record | 314 |  |
| [GeuvadisTranscriptExpr](/bioc/GeuvadisTranscriptExpr.md) Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project | Malgorzata Nowicka | experiment | 5 May 2026 | 295 | 0 |
| [networkBMA](/bioc/networkBMA.md) Regression-based network inference using Bayesian Model Averaging |  |  | no date on record | 239 |  |
| [curatedBreastData](/bioc/curatedBreastData.md) Curated breast cancer gene expression data with survival and treatment information | Levi Waldron | experiment | 23 Jul 2026 | 231 | 77 |
| [mammaPrintData](/bioc/mammaPrintData.md) RGLists from the Glas and Buyse breast cancer studies | Luigi Marchionni | experiment | 5 May 2026 | 222 | 0 |
| [ccdata](/bioc/ccdata.md) Data for Combination Connectivity Mapping (ccmap) Package | Alex Pickering | experiment | 5 May 2026 | 200 | 0 |

This page lists 1 to 22 of 22 packages.

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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=2.12&view=VariantAnnotation%2CBayesian%2CExpressionData, and every address is listed at /llms.txt.