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

# Packages

Search: "view:Normalization view:CancerData release:3.7"

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 3.7 (2018)
- biocViews term: Normalization
- biocViews term: CancerData
- Topic page: [Normalization](/topics/bioc/Normalization.md)
- Topic page: [CancerData](/topics/bioc/CancerData.md)

167 packages on Bioconductor tagged Normalization or CancerData, 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 |
| [DESeq2](/bioc/DESeq2.md) Differential gene expression analysis based on the negative binomial distribution | Michael Love | software | 28 Apr 2026 | 32,072 | 54 |
| [scater](/bioc/scater.md) Single-Cell Analysis Toolkit for Gene Expression Data in R | Alan O'Callaghan | software | 2 Jul 2026 | 12,635 | 78 |
| [sva](/bioc/sva.md) Surrogate Variable Analysis | Jeffrey T. Leek | software | 5 May 2026 | 10,804 | 68 |
| [scran](/bioc/scran.md) Methods for Single-Cell RNA-Seq Data Analysis | Aaron Lun | software | 28 Apr 2026 | 10,139 | 62 |
| [AUCell](/bioc/AUCell.md) AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures) | Gert Hulselmans | software | 29 Apr 2026 | 4,610 | 115 |
| [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 |
| [variancePartition](/bioc/variancePartition.md) Quantify and interpret drivers of variation in multilevel gene expression experiments | Gabriel E. Hoffman | software | 28 Apr 2026 | 3,211 | 99 |
| [metagenomeSeq](/bioc/metagenomeSeq.md) Statistical analysis for sparse high-throughput sequencing | Joseph N. Paulson | software | 28 Apr 2026 | 2,924 | 32 |
| [DiffBind](/bioc/DiffBind.md) Differential Binding Analysis of ChIP-Seq Peak Data | Rory Stark | software | 21 Jul 2026 | 2,490 | 141 |
| [bcellViper](/bioc/bcellViper.md) Human B-cell transcriptional interactome and normal human B-cell expression data | Mariano Javier Alvarez | experiment | 5 May 2026 | 2,177 | 7 |
| [missMethyl](/bioc/missMethyl.md) Analysing Illumina HumanMethylation BeadChip Data | Belinda Phipson | software | 12 May 2026 | 1,987 | 169 |
| [ChAMP](/bioc/ChAMP.md) Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC | Yuan Tian | software | 28 Apr 2026 | 1,643 | 266 |
| [MSstats](/bioc/MSstats.md) Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments | Meena Choi | software | 28 Apr 2026 | 1,586 | 100 |
| [csaw](/bioc/csaw.md) ChIP-Seq Analysis with Windows | Aaron Lun | software | 28 Apr 2026 | 1,536 | 46 |
| [Cardinal](/bioc/Cardinal.md) A mass spectrometry imaging toolbox for statistical analysis | Kylie Ariel Bemis | software | 28 Apr 2026 | 1,405 | 31 |
| [ACME](/bioc/ACME.md) Algorithms for Calculating Microarray Enrichment (ACME) | Sean Davis | software | 28 Apr 2026 | 1,278 | 7 |
| [CATALYST](/bioc/CATALYST.md) Cytometry dATa anALYSis Tools | Helena L. Crowell | software | 28 Apr 2026 | 1,265 | 176 |
| [quantro](/bioc/quantro.md) A test for when to use quantile normalization | Stephanie Hicks | software | 28 Apr 2026 | 1,244 | 153 |
| [singleCellTK](/bioc/singleCellTK.md) Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data | Joshua David Campbell | software | 29 Apr 2026 | 1,218 | 392 |
| [golubEsets](/bioc/golubEsets.md) exprSets for golub leukemia data | Vince Carey | experiment | 5 May 2026 | 1,207 | 7 |
| [BASiCS](/bioc/BASiCS.md) Bayesian Analysis of Single-Cell Sequencing data | Catalina Vallejos | software | 29 Apr 2026 | 1,206 | 129 |
| [affylmGUI](/bioc/affylmGUI.md) GUI for limma Package with Affymetrix Microarrays | Gordon Smyth | software | 28 Apr 2026 | 1,194 | 55 |
| [gCrisprTools](/bioc/gCrisprTools.md) Suite of Functions for Pooled Crispr Screen QC and Analysis | Russell Bainer | software | 28 Apr 2026 | 1,174 | 81 |
| [limmaGUI](/bioc/limmaGUI.md) GUI for limma Package With Two Color Microarrays | Gordon Smyth | software | 28 Apr 2026 | 1,165 | 11 |
| [diffHic](/bioc/diffHic.md) Differential Analysis of Hi-C Data | Aaron Lun | software | 28 Apr 2026 | 1,159 | 74 |
| [HiCcompare](/bioc/HiCcompare.md) HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets | Mikhail Dozmorov | software | 28 Apr 2026 | 1,151 | 74 |
| [HTSFilter](/bioc/HTSFilter.md) Filter replicated high-throughput transcriptome sequencing data | Andrea Rau | software | 28 Apr 2026 | 1,128 | 58 |

This page lists 1 to 30 of 167 packages. [Next](/packages.md?catalogue=bioc&release=3.7&view=Normalization%2CCancerData&sort=downloads&page=2)

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