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Topic: AnnotationData or Pathways or Clustering

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Release: Release 3.13 (2021)

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1,311 packages on Bioconductor tagged AnnotationData or Pathways or Clustering, most distinct IPs first

AnnotationData, Pathways and Clustering in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
KEGGREST
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)Bioconductor Package Maintainer		Bioconductor Package Maintainersoftware18 Jun 202645,88624
GenomeInfoDbData
Species and taxonomy ID look up tables used by GenomeInfoDbBioconductor Maintainer		Bioconductor Maintainerannotationno date on record36,7970
ggtree
an R package for visualization of tree and annotation dataGuangchuang Yu		Guangchuang Yusoftware29 Oct 202634,37279
GO.db
A set of annotation maps describing the entire Gene OntologyBioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record33,69442
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
treeio
Base Classes and Functions for Phylogenetic Tree Input and OutputGuangchuang Yu		Guangchuang Yusoftware30 Apr 202631,96639
enrichplot
Visualization of Functional Enrichment ResultGuangchuang Yu		Guangchuang Yusoftware28 Sep 202630,370128
org.Hs.eg.db
Genome wide annotation for HumanBioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record29,81342
clusterProfiler
A Universal Enrichment Tool for Interpreting Omics DataGuangchuang Yu		Guangchuang Yusoftware19 Oct 202629,661138
DOSE
Disease Ontology Semantic and Enrichment analysisGuangchuang Yu		Guangchuang Yusoftware28 Apr 202628,87377
fgsea
Fast Gene Set Enrichment AnalysisAlexey Sergushichev		Alexey Sergushichevsoftware28 Apr 202628,66038
GOSemSim
GO-terms Semantic Similarity MeasuresGuangchuang Yu		Guangchuang Yusoftware30 Jun 202627,49548
annotate
Annotation for microarraysBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202622,55744
BiocNeighbors
Nearest Neighbor Detection for Bioconductor PackagesAaron Lun		Aaron Lunsoftware28 Apr 202616,61924
org.Mm.eg.db
Genome wide annotation for MouseBioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record13,52042
GSEABase
Gene set enrichment data structures and methodsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202613,34446
GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo		Robert Castelosoftware25 Oct 202612,75897
ensembldb
Utilities to create and use Ensembl-based annotation databasesJohannes Rainer		Johannes Rainersoftware25 May 202611,00080
bluster
Clustering Algorithms for BioconductorAaron Lun		Aaron Lunsoftware28 Apr 202610,90344
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
phyloseq
Handling and analysis of high-throughput microbiome census dataPaul J. McMurdie		Paul J. McMurdiesoftware28 Apr 20268,37966
reactome.db
A set of annotation maps for reactomeWillem Ligtenberg		Willem Ligtenbergannotationno date on record7,57842
graphite
GRAPH Interaction from pathway Topological EnvironmentGabriele Sales		Gabriele Salessoftware28 Apr 20267,01248
KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorJitao David Zhang		Jitao David Zhangsoftware28 Apr 20266,80714
SingleR
Reference-Based Single-Cell RNA-Seq AnnotationAaron Lun		Aaron Lunsoftware10 Sep 20266,76128
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,750103
ReactomePA
Reactome Pathway AnalysisGuangchuang Yu		Guangchuang Yusoftware28 Apr 20266,720141
DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataMartin Morgan		Martin Morgansoftware28 Sep 20266,4909