Packages
230 packages on Bioconductor tagged Normalization or ChipDb or SystemsBiology, most distinct IPs first
Normalization, ChipDb and SystemsBiology 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 |
| sva Surrogate Variable AnalysisJeffrey T. Leek | Jeffrey T. Leek | software | 5 May 2026 | 10,804 | 68 |
| pathview a tool set for pathway based data integration and visualizationWeijun Luo | Weijun Luo | software | 28 Apr 2026 | 5,706 | 50 |
| hgu133plus2.db Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)Bioconductor Package Maintainer | Bioconductor Package Maintainer | annotation | no date on record | 4,227 | 43 |
| minfi Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen | Kasper Daniel Hansen | software | 28 Apr 2026 | 4,041 | 143 |
| topGO Enrichment Analysis for Gene OntologyFederico Marini | Federico Marini | software | 28 Apr 2026 | 3,228 | 48 |
| metagenomeSeq Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson | Joseph N. Paulson | software | 28 Apr 2026 | 2,924 | 32 |
| DiffBind Differential Binding Analysis of ChIP-Seq Peak DataRory Stark | Rory Stark | software | 21 Jul 2026 | 2,490 | 141 |
| viper Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez | Mariano J Alvarez | software | 28 Apr 2026 | 2,060 | 87 |
| hgu133a.db Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)Bioconductor Package Maintainer | Bioconductor Package Maintainer | annotation | no date on record | 1,996 | 43 |
| missMethyl Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson | Belinda Phipson | software | 12 May 2026 | 1,987 | 169 |
| gage Generally Applicable Gene-set Enrichment for Pathway AnalysisWeijun Luo | Weijun Luo | software | 28 Apr 2026 | 1,929 | 44 |
| ChAMP Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICYuan Tian | Yuan Tian | software | 28 Apr 2026 | 1,643 | 266 |
| hgu95av2.db Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)Bioconductor Package Maintainer | Bioconductor Package Maintainer | annotation | no date on record | 1,605 | 43 |
| 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 |
| csaw ChIP-Seq Analysis with WindowsAaron Lun | Aaron Lun | software | 28 Apr 2026 | 1,536 | 46 |
| Cardinal A mass spectrometry imaging toolbox for statistical analysisKylie Ariel Bemis | Kylie Ariel Bemis | software | 28 Apr 2026 | 1,405 | 31 |
| hpar Human Protein Atlas in RLaurent Gatto | Laurent Gatto | software | 28 Apr 2026 | 1,382 | 64 |
| RedeR Interactive visualization and manipulation of nested networksMauro Castro | Mauro Castro | software | 14 Jul 2026 | 1,317 | 23 |
| hugene10sttranscriptcluster.db Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster)Biocore Package Maintainer | Biocore Package Maintainer | annotation | no date on record | 1,302 | 43 |
| ACME Algorithms for Calculating Microarray Enrichment (ACME)Sean Davis | Sean Davis | software | 28 Apr 2026 | 1,278 | 7 |
| illuminaHumanv4.db Illumina HumanHT12v4 annotation data (chip illuminaHumanv4)Mark Dunning | Mark Dunning | annotation | no date on record | 1,274 | 43 |
| quantro A test for when to use quantile normalizationStephanie Hicks | Stephanie Hicks | software | 28 Apr 2026 | 1,244 | 153 |
| affylmGUI GUI for limma Package with Affymetrix MicroarraysGordon Smyth | Gordon Smyth | software | 28 Apr 2026 | 1,194 | 55 |
| limmaGUI GUI for limma Package With Two Color MicroarraysGordon Smyth | Gordon Smyth | software | 28 Apr 2026 | 1,165 | 11 |
| diffHic Differential Analysis of Hi-C DataAaron Lun | Aaron Lun | software | 28 Apr 2026 | 1,159 | 74 |
| RankProd Rank Product method for identifying differentially expressed genes with application in meta-analysisFrancesco Del Carratore | Francesco Del Carratore | software | 28 Apr 2026 | 1,142 | 6 |
| HTSFilter Filter replicated high-throughput transcriptome sequencing dataAndrea Rau | Andrea Rau | software | 28 Apr 2026 | 1,128 | 58 |