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Topic: VariantAnnotation or Bayesian or Normalization

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Release: Release 3.15 (2022)

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250 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
scuttle
Legacy Utilities for Single-Cell RNA-Seq AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202613,59139
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
apeglm
Approximate posterior estimation for GLM coefficientsAnqi Zhu		Anqi Zhusoftware28 Apr 20267,16136
batchelor
Single-Cell Batch Correction MethodsAaron Lun		Aaron Lunsoftware28 Apr 20265,56156
AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans		Gert Hulselmanssoftware29 Apr 20264,433115
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
ANCOMBC
Microbiome differential abudance and correlation analyses with bias correctionHuang Lin		Huang Linsoftware28 Apr 20262,784130
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
infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq DataChristophe Georgescu		Christophe Georgescusoftware28 Apr 20262,517194
Wrench
Wrench normalization for sparse count dataHector Corrada Bravo		Hector Corrada Bravosoftware28 Apr 20262,49311
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
celda
CEllular Latent Dirichlet AllocationJoshua Campbell		Joshua Campbellsoftware28 Apr 20262,011127
missMethyl
Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson		Belinda Phipsonsoftware12 May 20261,816169
MOFA2
Multi-Omics Factor Analysis v2Ricard Argelaguet		Ricard Argelaguetsoftware6 Sep 20261,79185
Maaslin2
"Multivariable Association Discovery in Population-scale Meta-omics Studies"Sagun Maharjan		Sagun Maharjansoftware28 Apr 20261,550133
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
fishpond
Fishpond: downstream methods and tools for expression dataMichael Love		Michael Lovesoftware28 Apr 20261,22954