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

# Packages

Search: "view:Transcription view:Clustering view:Metabolomics release:1.9"

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
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- `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 1.9 (2006)
- biocViews term: Transcription
- biocViews term: Clustering
- biocViews term: Metabolomics
- Topic page: [Transcription](/topics/bioc/Transcription.md)
- Topic page: [Clustering](/topics/bioc/Clustering.md)
- Topic page: [Metabolomics](/topics/bioc/Metabolomics.md)

20 packages on Bioconductor tagged Transcription or Clustering or Metabolomics, 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 |
| [xcms](/bioc/xcms.md) LC-MS and GC-MS Data Analysis | Steffen Neumann | software | 7 Jul 2026 | 3,537 | 143 |
| [Mfuzz](/bioc/Mfuzz.md) Soft clustering of omics time series data | Matthias Futschik | software | 28 Apr 2026 | 2,353 | 16 |
| [MLInterfaces](/bioc/MLInterfaces.md) Uniform interfaces to R machine learning procedures for data in Bioconductor containers | Vincent Carey | software | 28 Apr 2026 | 1,628 | 120 |
| [hopach](/bioc/hopach.md) Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) | Katherine S. Pollard | software | 28 Apr 2026 | 1,337 | 9 |
| [EBarrays](/bioc/EBarrays.md) Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification | Ming Yuan | software | 28 Apr 2026 | 1,284 | 11 |
| [made4](/bioc/made4.md) Multivariate analysis of microarray data using ADE4 | Aedin Culhane | software | 28 Apr 2026 | 1,279 | 38 |
| [affylmGUI](/bioc/affylmGUI.md) GUI for limma Package with Affymetrix Microarrays | Gordon Smyth | software | 28 Apr 2026 | 1,194 | 55 |
| [RankProd](/bioc/RankProd.md) Rank Product method for identifying differentially expressed genes with application in meta-analysis | Francesco Del Carratore | software | 28 Apr 2026 | 1,142 | 6 |
| [altcdfenvs](/bioc/altcdfenvs.md) alternative CDF environments (aka probeset mappings) | Laurent Gautier | software | 28 Apr 2026 | 1,113 | 23 |
| [adSplit](/bioc/adSplit.md) Annotation-Driven Clustering | Claudio Lottaz | software | 28 Apr 2026 | 1,072 | 51 |
| [bioDist](/bioc/bioDist.md) Different distance measures | Bioconductor Package Maintainer | software | 28 Apr 2026 | 1,000 | 8 |
| [ctc](/bioc/ctc.md) Cluster and Tree Conversion. | Antoine Lucas | software | 28 Apr 2026 | 979 | 1 |
| [clusterStab](/bioc/clusterStab.md) Compute cluster stability scores for microarray data | James W. MacDonald | software | 28 Apr 2026 | 894 | 7 |
| [geneRecommender](/bioc/geneRecommender.md) A gene recommender algorithm to identify genes coexpressed with a query set of genes | Greg Hather | software | 28 Apr 2026 | 821 | 7 |
| [MantelCorr](/bioc/MantelCorr.md) Compute Mantel Cluster Correlations | Brian Steinmeyer | software | 28 Apr 2026 | 760 | 1 |
| [maanova](/bioc/maanova.md) Tools for analyzing Micro Array experiments |  |  | no date on record | 541 |  |
| [simpleaffy](/bioc/simpleaffy.md) Very simple high level analysis of Affymetrix data |  |  | no date on record | 517 |  |
| [SAGx](/bioc/SAGx.md) Statistical Analysis of the GeneChip |  |  | no date on record | 447 |  |
| [splicegear](/bioc/splicegear.md) splicegear |  |  | no date on record | 372 |  |

This page lists 1 to 20 of 20 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=1.9&view=Transcription%2CClustering%2CMetabolomics, and every address is listed at /llms.txt.