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# Packages

Search: "view:SingleCell view:Transcriptomics release:3.0"

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 3.0 (2014)
- biocViews term: SingleCell
- biocViews term: Transcriptomics
- Topic page: [SingleCell](/topics/bioc/SingleCell.md)
- Topic page: [Transcriptomics](/topics/bioc/Transcriptomics.md)

6 packages on Bioconductor tagged SingleCell or Transcriptomics, 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 | 45,965 | 6 |
| [edgeR](/bioc/edgeR.md) Empirical Analysis of Digital Gene Expression Data in R | Yunshun Chen | software | 19 Oct 2026 | 32,392 | 10 |
| [topGO](/bioc/topGO.md) Enrichment Analysis for Gene Ontology | Federico Marini | software | 28 Apr 2026 | 3,228 | 48 |
| [Rsubread](/bioc/Rsubread.md) Mapping, quantification and variant analysis of sequencing data | Wei Shi | software | 28 Apr 2026 | 2,951 | 8 |
| [ALDEx2](/bioc/ALDEx2.md) Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account | Greg Gloor | software | 28 Apr 2026 | 2,533 | 56 |
| [made4](/bioc/made4.md) Multivariate analysis of microarray data using ADE4 | Aedin Culhane | software | 28 Apr 2026 | 1,279 | 38 |

This page lists 1 to 6 of 6 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=3.0&view=SingleCell%2CTranscriptomics, and every address is listed at /llms.txt.