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Topic: VariantAnnotation or Bayesian or Normalization

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Release: Release 3.4 (2016)

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102 packages on Bioconductor tagged VariantAnnotation or Bayesian or Normalization, most distinct IPs first

VariantAnnotation, Bayesian and Normalization 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
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202611,87478
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
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 20269,39162
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,21410
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20263,714143
maftools
Summarize, Analyze and Visualize MAF FilesAnand Mayakonda		Anand Mayakondasoftware28 Apr 20263,41926
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20262,89599
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
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,194141
missMethyl
Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson		Belinda Phipsonsoftware12 May 20261,816169
ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICYuan Tian		Yuan Tiansoftware28 Apr 20261,448266
MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics ExperimentsMeena Choi		Meena Choisoftware28 Apr 20261,385100
csaw
ChIP-Seq Analysis with WindowsAaron Lun		Aaron Lunsoftware28 Apr 20261,32746
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
quantro
A test for when to use quantile normalizationStephanie Hicks		Stephanie Hickssoftware28 Apr 20261,046153
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
ACME
Algorithms for Calculating Microarray Enrichment (ACME)Sean Davis		Sean Davissoftware28 Apr 20261,0107
HTSFilter
Filter replicated high-throughput transcriptome sequencing dataAndrea Rau		Andrea Rausoftware28 Apr 202698258
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 202696755
diffHic
Differential Analysis of Hi-C DataAaron Lun		Aaron Lunsoftware28 Apr 202696274
podkat
Position-Dependent Kernel Association TestUlrich Bodenhofer		Ulrich Bodenhofersoftware28 Apr 202694659