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Topic: Spatial or GeneRegulation or Annotation

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Release: Release 3.4 (2016)

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136 packages on Bioconductor tagged Spatial or GeneRegulation or Annotation, most distinct IPs first

Spatial, GeneRegulation and Annotation in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
GenomicRanges
Representation and manipulation of genomic intervalsHervé Pagès		Hervé Pagèssoftware28 Apr 202656,97410
SummarizedExperiment
A container (S4 class) for matrix-like assaysHervé Pagès		Hervé Pagèssoftware28 Apr 202653,48424
AnnotationDbi
Manipulation of SQLite-based annotations in BioconductorBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202647,94141
KEGGREST
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)Bioconductor Package Maintainer		Bioconductor Package Maintainersoftware18 Jun 202645,88624
GenomeInfoDb
Utilities for manipulating chromosome names, including modifying them to follow a particular naming styleHervé Pagès		Hervé Pagèssoftware28 Apr 202637,35620
ggtree
an R package for visualization of tree and annotation dataGuangchuang Yu		Guangchuang Yusoftware29 Oct 202634,37279
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
GOSemSim
GO-terms Semantic Similarity MeasuresGuangchuang Yu		Guangchuang Yusoftware30 Jun 202627,49548
rtracklayer
R interface to genome annotation files and the UCSC genome browserMichael Lawrence		Michael Lawrencesoftware28 Apr 202626,11956
biomaRt
Interface to BioMart databases (i.e. Ensembl)Hugo Gruson		Hugo Grusonsoftware28 Apr 202624,57161
annotate
Annotation for microarraysBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202622,55744
HDF5Array
HDF5 datasets as array-like objects in RHervé Pagès		Hervé Pagèssoftware28 Apr 202620,53728
GenomicFeatures
Query the gene models of a given organism/assemblyH. Pagès		H. Pagèssoftware28 Apr 202619,21874
BSgenome
Software infrastructure for efficient representation of full genomes and their SNPsHervé Pagès		Hervé Pagèssoftware28 Apr 202614,37557
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,66476
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
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu		Guangchuang Yusoftware28 Apr 20263,962158
OrganismDbi
Software to enable the smooth interfacing of different database packagesBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20263,44478
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,22848
AnnotationForge
Tools for building SQLite-based annotation data packagesBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20263,13145
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
CNEr
CNE Detection and VisualizationBoris Lenhard		Boris Lenhardsoftware28 Apr 20262,692112
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
GOstats
Tools for manipulating GO and microarraysBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20262,43763
goseq
Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini		Federico Marinisoftware28 Apr 20262,404104
Category
Category AnalysisBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20262,35557
viper
Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 20262,06087