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Topic: AnnotationData or BSgenome or Sequencing

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Release: Release 3.1 (2015)

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1,138 packages on Bioconductor tagged AnnotationData or BSgenome or Sequencing, most distinct IPs first

AnnotationData, BSgenome and Sequencing in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
Biostrings
Efficient manipulation of biological stringsHervé Pagès		Hervé Pagèssoftware2 Sep 202658,96214
GenomicRanges
Representation and manipulation of genomic intervalsHervé Pagès		Hervé Pagèssoftware28 Apr 202656,97410
AnnotationDbi
Manipulation of SQLite-based annotations in BioconductorBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202647,94141
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
GenomeInfoDbData
Species and taxonomy ID look up tables used by GenomeInfoDbBioconductor Maintainer		Bioconductor Maintainerannotationno date on record36,7970
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
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202630,33728
org.Hs.eg.db
Genome wide annotation for HumanBioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record29,81342
Rhtslib
HTSlib high-throughput sequencing library as an R packageHervé Pagès		Hervé Pagèssoftware28 Apr 202628,0831
GenomicAlignments
Representation and manipulation of short genomic alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 202627,00641
ComplexHeatmap
Make Complex HeatmapsZuguang Gu		Zuguang Gusoftware28 Apr 202623,95129
GenomicFeatures
Query the gene models of a given organism/assemblyH. Pagès		H. Pagèssoftware28 Apr 202619,21874
org.Mm.eg.db
Genome wide annotation for MouseBioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record13,52042
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
sva
Surrogate Variable AnalysisJeffrey T. Leek		Jeffrey T. Leeksoftware5 May 202610,80468
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,66476
phyloseq
Handling and analysis of high-throughput microbiome census dataPaul J. McMurdie		Paul J. McMurdiesoftware28 Apr 20268,37966
ShortRead
FASTQ input and manipulationBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20268,12653
reactome.db
A set of annotation maps for reactomeWillem Ligtenberg		Willem Ligtenbergannotationno date on record7,57842
DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataMartin Morgan		Martin Morgansoftware28 Sep 20266,4909
TxDb.Hsapiens.UCSC.hg19.knownGene
Annotation package for TxDb object(s)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record6,25875
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,70650
HDO.db
A set of annotation maps describing the entire Human Disease OntologyErqiang Hu		Erqiang Huannotationno date on record5,27742
BSgenome.Hsapiens.UCSC.hg38
Full genomic sequences for Homo sapiens (UCSC genome hg38)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record4,98960
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,88216
Gviz
Plotting data and annotation information along genomic coordinatesRobert Ivanek		Robert Ivaneksoftware28 Apr 20264,687150
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574