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Topic: AnnotationData or Sequencing

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Release: Release 3.20 (2024)

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1,814 packages on Bioconductor tagged AnnotationData or Sequencing, most distinct IPs first

AnnotationData 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
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
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
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
scuttle
Legacy Utilities for Single-Cell RNA-Seq AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202614,23639
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
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
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
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,66476
pwalign
Perform pairwise sequence alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 20269,39215
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
biomformat
An interface package for the BIOM file formatPaul J. McMurdie		Paul J. McMurdiesoftware28 Apr 20267,8379
apeglm
Approximate posterior estimation for GLM coefficientsAnqi Zhu		Anqi Zhusoftware28 Apr 20267,71636
EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labelingJared Andrews		Jared Andrewssoftware28 Apr 20267,62025