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

# Packages

Search: "view:ExperimentData view:DataRepresentation view:DNAMethylation release:3.16"

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 3.16 (2022)
- biocViews term: ExperimentData
- biocViews term: DataRepresentation
- biocViews term: DNAMethylation
- Topic page: [ExperimentData](/topics/bioc/ExperimentData.md)
- Topic page: [DataRepresentation](/topics/bioc/DataRepresentation.md)
- Topic page: [DNAMethylation](/topics/bioc/DNAMethylation.md)

639 packages on Bioconductor tagged ExperimentData or DataRepresentation or DNAMethylation, 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 |
| --- | --- | --- | --- | ---: | ---: |
| [S4Vectors](/bioc/S4Vectors.md) Foundation of vector-like and list-like containers in Bioconductor | Hervé Pagès | software | 16 Sep 2026 | 74,754 | 7 |
| [IRanges](/bioc/IRanges.md) Foundation of integer range manipulation in Bioconductor | Hervé Pagès | software | 28 Apr 2026 | 68,817 | 8 |
| [XVector](/bioc/XVector.md) Foundation of external vector representation and manipulation in Bioconductor | Hervé Pagès | software | 28 Apr 2026 | 63,837 | 10 |
| [Biostrings](/bioc/Biostrings.md) Efficient manipulation of biological strings | Hervé Pagès | software | 2 Sep 2026 | 58,962 | 14 |
| [DelayedArray](/bioc/DelayedArray.md) A unified framework for working transparently with on-disk and in-memory array-like datasets | Hervé Pagès | software | 26 May 2026 | 57,500 | 20 |
| [GenomicRanges](/bioc/GenomicRanges.md) Representation and manipulation of genomic intervals | Hervé Pagès | software | 28 Apr 2026 | 56,974 | 10 |
| [GenomeInfoDb](/bioc/GenomeInfoDb.md) Utilities for manipulating chromosome names, including modifying them to follow a particular naming style | Hervé Pagès | software | 28 Apr 2026 | 37,356 | 20 |
| [ggtree](/bioc/ggtree.md) an R package for visualization of tree and annotation data | Guangchuang Yu | software | 29 Oct 2026 | 34,372 | 79 |
| [edgeR](/bioc/edgeR.md) Empirical Analysis of Digital Gene Expression Data in R | Yunshun Chen | software | 19 Oct 2026 | 32,392 | 10 |
| [treeio](/bioc/treeio.md) Base Classes and Functions for Phylogenetic Tree Input and Output | Guangchuang Yu | software | 30 Apr 2026 | 31,966 | 39 |
| [SingleCellExperiment](/bioc/SingleCellExperiment.md) S4 Classes for Single Cell Data | Davide Risso | software | 28 Apr 2026 | 24,483 | 25 |
| [beachmat](/bioc/beachmat.md) Compiling Bioconductor to Handle Each Matrix Type | Aaron Lun | software | 28 Apr 2026 | 22,121 | 23 |
| [sparseMatrixStats](/bioc/sparseMatrixStats.md) Summary Statistics for Rows and Columns of Sparse Matrices | Constantin Ahlmann-Eltze | software | 28 Apr 2026 | 21,500 | 11 |
| [HDF5Array](/bioc/HDF5Array.md) HDF5 datasets as array-like objects in R | Hervé Pagès | software | 28 Apr 2026 | 20,537 | 28 |
| [DelayedMatrixStats](/bioc/DelayedMatrixStats.md) Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects | Peter Hickey | software | 28 Apr 2026 | 19,969 | 23 |
| [ScaledMatrix](/bioc/ScaledMatrix.md) Creating a DelayedMatrix of Scaled and Centered Values | Aaron Lun | software | 28 Apr 2026 | 17,725 | 21 |
| [BSgenome](/bioc/BSgenome.md) Software infrastructure for efficient representation of full genomes and their SNPs | Hervé Pagès | software | 28 Apr 2026 | 14,375 | 57 |
| [scater](/bioc/scater.md) Single-Cell Analysis Toolkit for Gene Expression Data in R | Alan O'Callaghan | software | 2 Jul 2026 | 12,635 | 78 |
| [SpatialExperiment](/bioc/SpatialExperiment.md) S4 Class for Spatially Resolved -omics Data | Dario Righelli | software | 28 Apr 2026 | 10,718 | 64 |
| [MultiAssayExperiment](/bioc/MultiAssayExperiment.md) Software for the integration of multi-omics experiments in Bioconductor | Marcel Ramos | software | 28 Apr 2026 | 9,523 | 45 |
| [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 |
| [TCGAbiolinksGUI.data](/bioc/TCGAbiolinksGUI.data.md) Data for the TCGAbiolinksGUI package | Tiago Chedraoui Silva | experiment | 5 May 2026 | 5,758 | 0 |
| [celldex](/bioc/celldex.md) Index of Reference Cell Type Datasets | Aaron Lun | experiment | 5 May 2026 | 5,717 | 95 |
| [ResidualMatrix](/bioc/ResidualMatrix.md) Creating a DelayedMatrix of Regression Residuals | Aaron Lun | software | 28 Apr 2026 | 5,559 | 21 |
| [monocle](/bioc/monocle.md) Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq | Cole Trapnell | software | 28 Apr 2026 | 4,485 | 74 |
| [zellkonverter](/bioc/zellkonverter.md) Conversion Between scRNA-seq Objects | Luke Zappia | software | 29 Apr 2026 | 4,278 | 41 |
| [bumphunter](/bioc/bumphunter.md) Bump Hunter | Tamilselvi Guharaj | software | 28 Apr 2026 | 4,268 | 83 |
| [ALL](/bioc/ALL.md) A data package | Robert Gentleman | experiment | 5 May 2026 | 4,171 | 7 |
| [minfi](/bioc/minfi.md) Analyze Illumina Infinium DNA methylation arrays | Kasper Daniel Hansen | software | 28 Apr 2026 | 4,041 | 143 |
| [cytolib](/bioc/cytolib.md) C++ infrastructure for representing and interacting with the gated cytometry data | Mike Jiang | software | 28 Apr 2026 | 3,820 | 8 |

This page lists 1 to 30 of 639 packages. [Next](/packages.md?catalogue=bioc&release=3.16&view=ExperimentData%2CDataRepresentation%2CDNAMethylation&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=3.16&view=ExperimentData%2CDataRepresentation%2CDNAMethylation, and every address is listed at /llms.txt.