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Topic: VariantAnnotation or Bayesian or DimensionReduction

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Release: Release 3.19 (2024)

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202 packages on Bioconductor tagged VariantAnnotation or Bayesian or DimensionReduction, most distinct IPs first

VariantAnnotation, Bayesian and DimensionReduction in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
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
BiocSingular
Singular Value Decomposition for Bioconductor PackagesAaron Lun		Aaron Lunsoftware8 Oct 202618,20237
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202611,87478
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,77176
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,21410
apeglm
Approximate posterior estimation for GLM coefficientsAnqi Zhu		Anqi Zhusoftware28 Apr 20267,16136
maftools
Summarize, Analyze and Visualize MAF FilesAnand Mayakonda		Anand Mayakondasoftware28 Apr 20263,41926
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,7228
infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq DataChristophe Georgescu		Christophe Georgescusoftware28 Apr 20262,517194
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,31156
celda
CEllular Latent Dirichlet AllocationJoshua Campbell		Joshua Campbellsoftware28 Apr 20262,011127
Nebulosa
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density EstimationJose Alquicira-Hernandez		Jose Alquicira-Hernandezsoftware28 Apr 20261,90083
MOFA2
Multi-Omics Factor Analysis v2Ricard Argelaguet		Ricard Argelaguetsoftware6 Sep 20261,79185
zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq DataDavide Risso		Davide Rissosoftware28 Apr 20261,42674
GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessStephanie M. Gogarten		Stephanie M. Gogartensoftware28 Apr 20261,247117
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,17592
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,16820
iSEE
Interactive SummarizedExperiment ExplorerKevin Rue-Albrecht		Kevin Rue-Albrechtsoftware28 Apr 20261,091109
PureCN
Copy number calling and SNV classification using targeted short read sequencingMarkus Riester		Markus Riestersoftware28 Apr 20261,083101
made4
Multivariate analysis of microarray data using ADE4Aedin Culhane		Aedin Culhanesoftware28 Apr 20261,08238
densvis
Density-Preserving Data Visualization via Non-Linear Dimensionality ReductionAlan O'Callaghan		Alan O'Callaghansoftware28 Apr 20261,05826
Banksy
Spatial transcriptomic clusteringJoseph Lee		Joseph Leesoftware3 May 20261,042109
decontX
Decontamination of single cell genomics dataJoshua Campbell		Joshua Campbellsoftware28 Apr 20261,040233
puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)Xuejun Liu		Xuejun Liusoftware28 Apr 20261,03355
scde
Single Cell Differential ExpressionEvan Biederstedt		Evan Biederstedtsoftware28 Apr 20261,03350
pcaExplorer
Interactive Visualization of RNA-seq Data Using a Principal Components ApproachFederico Marini		Federico Marinisoftware28 Apr 20261,003230
tricycle
tricycle: Transferable Representation and Inference of cell cycleShijie Zheng		Shijie Zhengsoftware28 Apr 20261,000111
BASiCS
Bayesian Analysis of Single-Cell Sequencing dataCatalina Vallejos		Catalina Vallejossoftware29 Apr 2026995129