Packages
217 packages on Bioconductor tagged Normalization or DimensionReduction, most distinct IPs first
Normalization and DimensionReduction in Topics
| Package | Maintainer | Category | Latest version | Distinct IPs a month | Needs |
|---|---|---|---|---|---|
| limma Linear Models for Microarray and Omics DataGordon Smyth | Gordon Smyth | software | 10 Aug 2026 | 45,965 | 6 |
| edgeR Empirical Analysis of Digital Gene Expression Data in RYunshun Chen | Yunshun Chen | software | 19 Oct 2026 | 32,392 | 10 |
| DESeq2 Differential gene expression analysis based on the negative binomial distributionMichael Love | Michael Love | software | 28 Apr 2026 | 32,072 | 54 |
| BiocSingular Singular Value Decomposition for Bioconductor PackagesAaron Lun | Aaron Lun | software | 8 Oct 2026 | 18,880 | 37 |
| scuttle Legacy Utilities for Single-Cell RNA-Seq AnalysisAaron Lun | Aaron Lun | software | 28 Apr 2026 | 14,236 | 39 |
| scater Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan | Alan O'Callaghan | software | 2 Jul 2026 | 12,635 | 78 |
| sva Surrogate Variable AnalysisJeffrey T. Leek | Jeffrey T. Leek | software | 5 May 2026 | 10,804 | 68 |
| scran Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun | Aaron Lun | software | 28 Apr 2026 | 10,139 | 62 |
| batchelor Single-Cell Batch Correction MethodsAaron Lun | Aaron Lun | software | 28 Apr 2026 | 5,720 | 56 |
| AUCell AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans | Gert Hulselmans | software | 29 Apr 2026 | 4,610 | 115 |
| minfi Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen | Kasper Daniel Hansen | software | 28 Apr 2026 | 4,041 | 143 |
| variancePartition Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman | Gabriel E. Hoffman | software | 28 Apr 2026 | 3,211 | 99 |
| ANCOMBC Microbiome differential abudance and correlation analyses with bias correctionHuang Lin | Huang Lin | software | 28 Apr 2026 | 3,000 | 130 |
| metagenomeSeq Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson | Joseph N. Paulson | software | 28 Apr 2026 | 2,924 | 32 |
| Wrench Wrench normalization for sparse count dataHector Corrada Bravo | Hector Corrada Bravo | software | 28 Apr 2026 | 2,619 | 11 |
| DiffBind Differential Binding Analysis of ChIP-Seq Peak DataRory Stark | Rory Stark | software | 21 Jul 2026 | 2,490 | 141 |
| Nebulosa Single-Cell Data Visualisation Using Kernel Gene-Weighted Density EstimationJose Alquicira-Hernandez | Jose Alquicira-Hernandez | software | 28 Apr 2026 | 2,000 | 83 |
| missMethyl Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson | Belinda Phipson | software | 12 May 2026 | 1,987 | 169 |
| MOFA2 Multi-Omics Factor Analysis v2Ricard Argelaguet | Ricard Argelaguet | software | 6 Sep 2026 | 1,967 | 85 |
| Maaslin2 "Multivariable Association Discovery in Population-scale Meta-omics Studies"Sagun Maharjan | Sagun Maharjan | software | 28 Apr 2026 | 1,690 | 133 |
| ChAMP Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICYuan Tian | Yuan Tian | software | 28 Apr 2026 | 1,643 | 266 |
| MSstats Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics ExperimentsMeena Choi | Meena Choi | software | 28 Apr 2026 | 1,586 | 100 |
| zinbwave Zero-Inflated Negative Binomial Model for RNA-Seq DataDavide Risso | Davide Risso | software | 28 Apr 2026 | 1,569 | 74 |
| csaw ChIP-Seq Analysis with WindowsAaron Lun | Aaron Lun | software | 28 Apr 2026 | 1,536 | 46 |
| GENESIS GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessStephanie M. Gogarten | Stephanie M. Gogarten | software | 28 Apr 2026 | 1,444 | 117 |
| Cardinal A mass spectrometry imaging toolbox for statistical analysisKylie Ariel Bemis | Kylie Ariel Bemis | software | 28 Apr 2026 | 1,405 | 31 |
| SC3 Single-Cell Consensus ClusteringVladimir Kiselev | Vladimir Kiselev | software | 28 Apr 2026 | 1,368 | 92 |
| fishpond Fishpond: downstream methods and tools for expression dataMichael Love | Michael Love | software | 28 Apr 2026 | 1,363 | 54 |
| made4 Multivariate analysis of microarray data using ADE4Aedin Culhane | Aedin Culhane | software | 28 Apr 2026 | 1,279 | 38 |
| ACME Algorithms for Calculating Microarray Enrichment (ACME)Sean Davis | Sean Davis | software | 28 Apr 2026 | 1,278 | 7 |