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Topic: VariantAnnotation or Bayesian or Classification

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Release: Release 3.3 (2016)

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121 packages on Bioconductor tagged VariantAnnotation or Bayesian or Classification, most distinct IPs first

VariantAnnotation, Bayesian and Classification 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
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
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,21410
DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataMartin Morgan		Martin Morgansoftware28 Sep 20266,1479
dada2
Accurate, high-resolution sample inference from amplicon sequencing dataBenjamin Callahan		Benjamin Callahansoftware28 Apr 20263,90075
interactiveDisplayBase
Base package for enabling powerful shiny web displays of Bioconductor objects		no date on record2,910
ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataEtienne A. Thevenot		Etienne A. Thevenotsoftware28 Apr 20262,73697
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,7228
metagenomeSeq
Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20262,72232
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,31156
fastseg
fastseg - a fast segmentation algorithmAlexander Blume		Alexander Blumesoftware28 Apr 20261,72813
MLInterfaces
Uniform interfaces to R machine learning procedures for data in Bioconductor containersVincent Carey		Vincent Careysoftware28 Apr 20261,417120
pRoloc
A unifying bioinformatics framework for spatial proteomicsLisa Breckels		Lisa Breckelssoftware28 Apr 20261,400230
genefu
Computation of Gene Expression-Based Signatures in Breast CancerBenjamin Haibe-Kains		Benjamin Haibe-Kainssoftware28 Apr 20261,358116
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
Cardinal
A mass spectrometry imaging toolbox for statistical analysisKylie Ariel Bemis		Kylie Ariel Bemissoftware28 Apr 20261,15731
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
AIMS
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular SubtypeEric R Paquet		Eric R Paquetsoftware28 Apr 20261,07711
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
iCOBRA
Comparison and Visualization of Ranking and Assignment MethodsCharlotte Soneson		Charlotte Sonesonsoftware28 Apr 20261,02782
ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testingDario Strbenac		Dario Strbenacsoftware28 Apr 20261,016147
GenVisR
Genomic Visualizations in RZachary Skidmore		Zachary Skidmoresoftware28 Apr 2026980113
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 202696755
cancerclass
Development and validation of diagnostic tests from high-dimensional molecular dataDaniel Kosztyla		Daniel Kosztylasoftware28 Apr 20269518