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Topic: VariantAnnotation or Bayesian or Sequencing

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Release: Release 3.2 (2015)

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317 packages on Bioconductor tagged VariantAnnotation or Bayesian or Sequencing, most distinct IPs first

VariantAnnotation, Bayesian and Sequencing in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
Biostrings
Efficient manipulation of biological stringsHervé Pagès		Hervé Pagèssoftware2 Sep 202657,90914
GenomicRanges
Representation and manipulation of genomic intervalsHervé Pagès		Hervé Pagèssoftware28 Apr 202656,12910
SummarizedExperiment
A container (S4 class) for matrix-like assaysHervé Pagès		Hervé Pagèssoftware28 Apr 202652,64024
AnnotationDbi
Manipulation of SQLite-based annotations in BioconductorBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202647,36841
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202644,6566
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202631,84554
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202631,06510
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202630,39628
Rhtslib
HTSlib high-throughput sequencing library as an R packageHervé Pagès		Hervé Pagèssoftware28 Apr 202627,6971
GenomicAlignments
Representation and manipulation of short genomic alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 202626,58341
ComplexHeatmap
Make Complex HeatmapsZuguang Gu		Zuguang Gusoftware28 Apr 202623,56729
GenomicFeatures
Query the gene models of a given organism/assemblyH. Pagès		H. Pagèssoftware28 Apr 202619,16374
GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq DataRobert Castelo		Robert Castelosoftware25 Oct 202612,44697
ensembldb
Utilities to create and use Ensembl-based annotation databasesJohannes Rainer		Johannes Rainersoftware25 May 202610,97280
sva
Surrogate Variable AnalysisJeffrey T. Leek		Jeffrey T. Leeksoftware5 May 202610,78668
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,77176
phyloseq
Handling and analysis of high-throughput microbiome census dataPaul J. McMurdie		Paul J. McMurdiesoftware28 Apr 20268,12266
ShortRead
FASTQ input and manipulationBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20267,81253
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,21410
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,713103
DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataMartin Morgan		Martin Morgansoftware28 Sep 20266,1479
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,66750
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,60316
Gviz
Plotting data and annotation information along genomic coordinatesRobert Ivanek		Robert Ivaneksoftware28 Apr 20264,416150
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,34774
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu		Guangchuang Yusoftware28 Apr 20263,660158
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,05548
interactiveDisplayBase
Base package for enabling powerful shiny web displays of Bioconductor objects		no date on record2,910
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20262,89599
msa
Multiple Sequence AlignmentUlrich Bodenhofer		Ulrich Bodenhofersoftware12 Aug 20262,82216