bioconductor.org "Bayesian" keyword
View the packages on the bioconductor.org package registry that are tagged with the "Bayesian" keyword.
Top 0.6% on bioconductor.org
26 versions - Latest release: about 1 month ago - 181 dependent packages - 4.24 million downloads total - 4 maintainers
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R26 versions - Latest release: about 1 month ago - 181 dependent packages - 4.24 million downloads total - 4 maintainers
BUMHMM 1.34.0
Computational pipeline for computing probability of modification from structure probing experimen...6 versions - Latest release: 2 months ago - 16.7 thousand downloads total - 1 maintainer
GRENITS 1.62.0
Gene Regulatory Network Inference Using Time Series6 versions - Latest release: 2 months ago - 30 thousand downloads total - 1 maintainer
Top 0.5% on bioconductor.org
11 versions - Latest release: 3 months ago - 146 dependent packages - 4.17 million downloads total - 330 stars on GitHub - 1 maintainer
DESeq2 1.50.2
Differential gene expression analysis based on the negative binomial distribution11 versions - Latest release: 3 months ago - 146 dependent packages - 4.17 million downloads total - 330 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
16 versions - Latest release: 3 months ago - 322 dependent packages - 6.92 million downloads total - 1 maintainer
limma 3.66.0
Linear Models for Microarray and Omics Data16 versions - Latest release: 3 months ago - 322 dependent packages - 6.92 million downloads total - 1 maintainer
bandle 1.14.0
An R package for the Bayesian analysis of differential subcellular localisation experiments6 versions - Latest release: 3 months ago - 8.17 thousand downloads total - 4 stars on GitHub - 1 maintainer
AMARETTO 1.26.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...6 versions - Latest release: 3 months ago - 16.9 thousand downloads total - 1 maintainer
ctsGE 1.36.0
Clustering of Time Series Gene Expression data6 versions - Latest release: 2 months ago - 17.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
DEqMS 1.28.0
a tool to perform statistical analysis of differential protein expression for quantitative proteo...6 versions - Latest release: 3 months ago - 28.8 thousand downloads total - 17 stars on GitHub - 1 maintainer
NormalyzerDE 1.28.0
Evaluation of normalization methods and calculation of differential expression analysis statistics6 versions - Latest release: 2 months ago - 25.3 thousand downloads total - 25 stars on GitHub - 1 maintainer
ClustIRR 1.8.0
Clustering of immune receptor repertoires5 versions - Latest release: 3 months ago - 5.81 thousand downloads total - 4 stars on GitHub - 1 maintainer
scMET 1.12.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity6 versions - Latest release: 2 months ago - 7.01 thousand downloads total - 18 stars on GitHub - 1 maintainer
wavClusteR 2.44.0
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data6 versions - Latest release: 2 months ago - 25.3 thousand downloads total - 1 maintainer
decontX 1.8.0
Decontamination of single cell genomics data6 versions - Latest release: 2 months ago - 15.7 thousand downloads total - 1 maintainer
CoGAPS 3.30.0
Coordinated Gene Activity in Pattern Sets6 versions - Latest release: 2 months ago - 3 dependent packages - 42.8 thousand downloads total - 4 maintainers
TRONCO 2.42.0
TRONCO, an R package for TRanslational ONCOlogy7 versions - Latest release: 2 months ago - 25.6 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
6 versions - Latest release: 2 months ago - 57.4 thousand downloads total - 1 maintainer
limmaGUI 1.86.0
GUI for limma Package With Two Color Microarrays6 versions - Latest release: 2 months ago - 57.4 thousand downloads total - 1 maintainer
R3CPET 1.42.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process7 versions - Latest release: 2 months ago - 19.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
6 versions - Latest release: 3 months ago - 19 dependent packages - 836 thousand downloads total - 53 stars on GitHub - 1 maintainer
pcaMethods 2.2.0
A collection of PCA methods6 versions - Latest release: 3 months ago - 19 dependent packages - 836 thousand downloads total - 53 stars on GitHub - 1 maintainer
tigre 1.64.0
Transcription factor Inference through Gaussian process Reconstruction of Expression6 versions - Latest release: 3 months ago - 34.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
BUScorrect 1.28.0
Batch Effects Correction with Unknown Subtypes6 versions - Latest release: 2 months ago - 12.3 thousand downloads total - 1 maintainer
graper 1.26.0
Adaptive penalization in high-dimensional regression and classification with external covariates ...7 versions - Latest release: 2 months ago - 11.8 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
6 versions - Latest release: 2 months ago - 1 dependent package - 55.8 thousand downloads total - 1 maintainer
puma 3.52.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...6 versions - Latest release: 2 months ago - 1 dependent package - 55.8 thousand downloads total - 1 maintainer
INTACT 1.10.0
Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis6 versions - Latest release: 3 months ago - 5.99 thousand downloads total - 17 stars on GitHub - 1 maintainer
BASiCS 2.22.0
Bayesian Analysis of Single-Cell Sequencing data6 versions - Latest release: 3 months ago - 2 dependent packages - 32.5 thousand downloads total - 84 stars on GitHub - 1 maintainer
scDDboost 1.12.0
A compositional model to assess expression changes from single-cell rna-seq data7 versions - Latest release: 3 months ago - 7.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
mfa 1.31.0
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations6 versions - Latest release: 2 months ago - 1 dependent package - 20.1 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
6 versions - Latest release: 3 months ago - 6 dependent packages - 156 thousand downloads total - 0 stars on GitHub - 1 maintainer
baySeq 2.44.0
Empirical Bayesian analysis of patterns of differential expression in count data6 versions - Latest release: 3 months ago - 6 dependent packages - 156 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
7 versions - Latest release: 2 months ago - 11 dependent packages - 460 thousand downloads total - 1 maintainer
apeglm 1.32.0
Approximate posterior estimation for GLM coefficients7 versions - Latest release: 2 months ago - 11 dependent packages - 460 thousand downloads total - 1 maintainer
phenopath 1.34.0
Genomic trajectories with heterogeneous genetic and environmental backgrounds6 versions - Latest release: 2 months ago - 1 dependent package - 21.8 thousand downloads total - 1 maintainer
ccfindR 1.30.0
Cancer Clone Finder6 versions - Latest release: 2 months ago - 1 dependent package - 18.7 thousand downloads total - 1 maintainer
BPRMeth 1.35.0
Model higher-order methylation profiles6 versions - Latest release: 2 months ago - 1 dependent package - 21 thousand downloads total - 1 maintainer
BayesKnockdown 1.36.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data6 versions - Latest release: 2 months ago - 17.6 thousand downloads total - 1 maintainer
GmicR 1.24.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...6 versions - Latest release: 2 months ago - 11.4 thousand downloads total - 1 maintainer
Clomial 1.46.0
Infers clonal composition of a tumor6 versions - Latest release: 3 months ago - 22.6 thousand downloads total - 1 maintainer
gemma.R 3.6.1
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...18 versions - Latest release: 7 days ago - 8.79 thousand downloads total - 10 stars on GitHub - 1 maintainer
retrofit 1.10.0
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics6 versions - Latest release: 3 months ago - 5.98 thousand downloads total - 3 stars on GitHub - 1 maintainer
KBoost 1.18.0
Inference of gene regulatory networks from gene expression data6 versions - Latest release: 2 months ago - 7.66 thousand downloads total - 4 stars on GitHub - 1 maintainer
MetaboDynamics 2.0.2
Bayesian analysis of longitudinal metabolomics data4 versions - Latest release: about 2 months ago - 3.24 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
7 versions - Latest release: 3 months ago - 161 thousand downloads total - 646 stars on GitHub - 1 maintainer
infercnv 1.26.0
Infer Copy Number Variation from Single-Cell RNA-Seq Data7 versions - Latest release: 3 months ago - 161 thousand downloads total - 646 stars on GitHub - 1 maintainer
OpenStats 1.22.0
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phen...6 versions - Latest release: 2 months ago - 9.39 thousand downloads total - 1 maintainer
bacon 1.38.0
Controlling bias and inflation in association studies using the empirical null distribution6 versions - Latest release: 2 months ago - 29.7 thousand downloads total - 1 maintainer
BASiCStan 1.12.0
Stan implementation of BASiCS6 versions - Latest release: 3 months ago - 7.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
cellmig 1.0.0
Uncertainty-aware quantitative analysis of high-throughput live cell migration data2 versions - Latest release: 2 months ago - 865 downloads total - 1 stars on GitHub - 1 maintainer
roastgsa 1.8.0
Rotation based gene set analysis5 versions - Latest release: 2 months ago - 5.48 thousand downloads total - 0 stars on GitHub - 1 maintainer
BANDITS 1.26.0
BANDITS: Bayesian ANalysis of DIfferenTial Splicing8 versions - Latest release: 3 months ago - 1 dependent package - 16.8 thousand downloads total - 18 stars on GitHub - 1 maintainer
HiLDA 1.24.0
Conducting statistical inference on comparing the mutational exposures of mutational signatures b...6 versions - Latest release: 3 months ago - 1 dependent package - 12 thousand downloads total - 3 stars on GitHub - 1 maintainer
CBN2Path 1.0.0
"CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjun...2 versions - Latest release: 2 months ago - 949 downloads total - 0 stars on GitHub - 1 maintainer
Top 7.5% on bioconductor.org
9 versions - Latest release: 2 months ago - 2 dependent packages - 77.3 thousand downloads total - 133 stars on GitHub - 1 maintainer
celda 1.26.0
CEllular Latent Dirichlet Allocation9 versions - Latest release: 2 months ago - 2 dependent packages - 77.3 thousand downloads total - 133 stars on GitHub - 1 maintainer
BG2 1.10.0
Performs Bayesian GWAS analysis for non-Gaussian data using BG26 versions - Latest release: 2 months ago - 6.2 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
6 versions - Latest release: 2 months ago - 77.7 thousand downloads total - 1 maintainer
affylmGUI 1.84.0
GUI for limma Package with Affymetrix Microarrays6 versions - Latest release: 2 months ago - 77.7 thousand downloads total - 1 maintainer
banocc 1.34.0
Bayesian ANalysis Of Compositional Covariance6 versions - Latest release: 2 months ago - 17.8 thousand downloads total - 2 maintainers
BUSseq 1.16.0
Batch Effect Correction with Unknow Subtypes for scRNA-seq data6 versions - Latest release: 3 months ago - 8.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
RIVER 1.34.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)6 versions - Latest release: 3 months ago - 15.9 thousand downloads total - 10 stars on GitHub - 1 maintainer
plasmut 1.8.0
Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic,...5 versions - Latest release: 2 months ago - 5.31 thousand downloads total - 1 maintainer
DMCFB 1.24.0
Differentially Methylated Cytosines via a Bayesian Functional Approach8 versions - Latest release: 2 months ago - 10.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
EBcoexpress 1.54.0
EBcoexpress for Differential Co-Expression Analysis6 versions - Latest release: 3 months ago - 1 dependent package - 31 thousand downloads total - 1 maintainer
CBNplot 1.10.0
plot bayesian network inferred from gene expression data based on enrichment analysis results8 versions - Latest release: 3 months ago - 8.94 thousand downloads total - 56 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
6 versions - Latest release: 3 months ago - 4 dependent packages - 143 thousand downloads total - 28 stars on GitHub - 1 maintainer
ALDEx2 1.42.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account6 versions - Latest release: 3 months ago - 4 dependent packages - 143 thousand downloads total - 28 stars on GitHub - 1 maintainer
rRDP 1.44.0
Interface to the RDP Classifier6 versions - Latest release: 3 months ago - 21.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
8 versions - Latest release: about 2 months ago - 65.1 thousand downloads total - 354 stars on GitHub - 1 maintainer
MOFA2 1.20.1
Multi-Omics Factor Analysis v28 versions - Latest release: about 2 months ago - 65.1 thousand downloads total - 354 stars on GitHub - 1 maintainer
BaalChIP 1.36.0
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes6 versions - Latest release: 3 months ago - 20.9 thousand downloads total - 1 maintainer
BAGS 2.50.0
A Bayesian Approach for Geneset Selection6 versions - Latest release: 3 months ago - 28.2 thousand downloads total - 1 maintainer
beer 1.14.1
Bayesian Enrichment Estimation in R6 versions - Latest release: 3 months ago - 8.31 thousand downloads total - 11 stars on GitHub - 1 maintainer
DifferentialRegulation 2.8.0
Differentially regulated genes from scRNA-seq data10 versions - Latest release: 3 months ago - 7.98 thousand downloads total - 11 stars on GitHub - 1 maintainer
MADSEQ 1.36.0
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data6 versions - Latest release: 3 months ago - 15.2 thousand downloads total - 4 stars on GitHub - 1 maintainer
SanityR 1.0.0
R/Bioconductor interface to the Sanity model gene expression analysis1 version - Latest release: 3 months ago - 946 downloads total - 2 stars on GitHub - 1 maintainer
PROPS 1.32.0
PRObabilistic Pathway Score (PROPS)7 versions - Latest release: 3 months ago - 14.1 thousand downloads total - 1 maintainer
limpa 1.2.4
Quantification and Differential Analysis of Proteomics Data6 versions - Latest release: 17 days ago - 3.75 thousand downloads total - 17 stars on GitHub - 1 maintainer
proDA 1.24.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data7 versions - Latest release: 3 months ago - 1 dependent package - 22.8 thousand downloads total - 16 stars on GitHub - 1 maintainer
protGear 1.14.0
Protein Micro Array Data Management and Interactive Visualization6 versions - Latest release: 3 months ago - 9.33 thousand downloads total - 1 stars on GitHub - 1 maintainer
normr 1.36.0
Normalization and difference calling in ChIP-seq data6 versions - Latest release: 2 months ago - 23.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
Melissa 1.25.0
Bayesian clustering and imputationa of single cell methylomes6 versions - Latest release: 2 months ago - 10.7 thousand downloads total - 1 maintainer
HiCPotts 1.0.0
HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C1 version - Latest release: 3 months ago - 799 downloads total - 0 stars on GitHub - 1 maintainer
ASSIGN 1.46.0
Adaptive Signature Selection and InteGratioN (ASSIGN)6 versions - Latest release: 2 months ago - 1 dependent package - 28.8 thousand downloads total - 2 stars on GitHub - 4 maintainers
omicplotR 1.30.0
Visual Exploration of Omic Datasets Using a Shiny App6 versions - Latest release: 2 months ago - 14.4 thousand downloads total - 1 maintainer
ternarynet 1.54.0
Ternary Network Estimation6 versions - Latest release: 2 months ago - 25.1 thousand downloads total - 1 maintainer
GWAS.BAYES 1.20.0
Bayesian analysis of Gaussian GWAS data6 versions - Latest release: 2 months ago - 8.98 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
6 versions - Latest release: 2 months ago - 73.9 thousand downloads total - 1 maintainer
scde 2.38.0
Single Cell Differential Expression6 versions - Latest release: 2 months ago - 73.9 thousand downloads total - 1 maintainer
covEB 1.36.0
Empirical Bayes estimate of block diagonal covariance matrices6 versions - Latest release: 2 months ago - 15.5 thousand downloads total - 1 maintainer
metaseqR2 1.22.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...6 versions - Latest release: 2 months ago - 11.5 thousand downloads total - 1 maintainer
IgGeneUsage 1.24.0
Differential gene usage in immune repertoires6 versions - Latest release: 3 months ago - 6 stars on GitHub - 1 maintainer
sccomp 2.2.0
Differential Composition and Variability Analysis for Single-Cell Data6 versions - Latest release: 3 months ago - 9.59 thousand downloads total - 112 stars on GitHub - 1 maintainer
gemini 1.24.0
GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens6 versions - Latest release: 3 months ago - 9.6 thousand downloads total - 15 stars on GitHub - 1 maintainer
STdeconvolve 1.12.0 removed
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data5 versions - Latest release: 9 months ago - 7.67 thousand downloads total - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: about 2 years ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
IntOMICS 1.4.0 removed
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: over 1 year ago - 1.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
scDD 1.28.0
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions3 versions - Latest release: over 1 year ago - 1 dependent package - 22.1 thousand downloads total - 33 stars on GitHub - 1 maintainer
ATACCoGAPS 1.8.0 removed
Analysis Tools for scATACseq Data with CoGAPS4 versions - Latest release: about 1 year ago - 2.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
RJMCMCNucleosomes 1.30.0
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-rea...4 versions - Latest release: about 1 year ago - 11.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
EBSeqHMM 1.38.0 removed
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments3 versions - Latest release: over 1 year ago - 17.8 thousand downloads total - 1 maintainer
BDMMAcorrect 1.22.0 removed
Meta-analysis for the metagenomic read counts data from different cohorts3 versions - Latest release: over 1 year ago - 6.75 thousand downloads total - 1 maintainer
sparseDOSSA 1.28.0 removed
Sparse Data Observations for Simulating Synthetic Abundance3 versions - Latest release: over 1 year ago - 8.65 thousand downloads total - 1 maintainer
CSSP 1.40.0 removed
ChIP-Seq Statistical Power2 versions - Latest release: about 2 years ago - 17.8 thousand downloads total
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: about 2 years ago - 7.94 thousand downloads total - 1 maintainer
IsoBayes 1.2.7
IsoBayes: Single Isoform protein inference Method via Bayesian Analyses5 versions - Latest release: over 1 year ago - 2.24 thousand downloads total - 7 stars on GitHub - 1 maintainer
hummingbird 1.14.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions3 versions - Latest release: over 1 year ago - 4.86 thousand downloads total - 1 maintainer
calm 1.18.0
Covariate Assisted Large-scale Multiple testing3 versions - Latest release: over 1 year ago - 5.83 thousand downloads total - 0 stars on GitHub - 1 maintainer
Related Keywords
Software
98
GeneExpression
51
ImmunoOncology
40
Sequencing
38
DifferentialExpression
34
RNASeq
32
Clustering
29
Regression
26
SingleCell
24
MultipleComparison
21
Transcriptomics
18
Transcription
18
StatisticalMethod
17
Normalization
17
Genetics
17
DataImport
16
BatchEffect
15
TimeCourse
13
Microarray
13
Preprocessing
13
Proteomics
12
BiomedicalInformatics
11
QualityControl
11
GeneRegulation
10
Network
10
Visualization
10
Coverage
10
GeneSetEnrichment
10
SystemsBiology
9
Classification
9
NetworkInference
8
GraphAndNetwork
8
ChIPSeq
8
CellBiology
8
DifferentialSplicing
8
FeatureExtraction
8
Epigenetics
8
AlternativeSplicing
8
mRNAMicroarray
7
FunctionalGenomics
7
Pathways
7
OneChannel
6
DNAMethylation
6
bioinformatics
5
Metagenomics
5
MassSpectrometry
5
HiddenMarkovModel
5
TwoChannel
5
ProprietaryPlatforms
5
Microbiome
5
DifferentialMethylation
5
Metabolomics
5
ExonArray
5
bayesian
5
GUI
4
r
4
KEGG
4
Spatial
4
SomaticMutation
4
GenomeWideAssociation
4
DimensionReduction
4
MicroRNAArray
4
CopyNumberVariation
4
GeneticVariability
3
PrincipalComponent
3
single-cell
3
DNASeq
3
ExperimentalDesign
3
GenomicVariation
3
SNP
3
bioconductor
3
FunctionalPrediction
2
differential-expression
2
transcriptomics
2
VariantDetection
2
PeakDetection
2
GeneTarget
2
Survival
2
r-package
2
BiologicalQuestion
2
GenePrediction
2
AssayDomain
2
Alignment
2
SAGE
2
Cheminformatics
2
MethylationArray
2
limma
2
MathematicalBiology
2
b-cell-receptor
2
clustering
2
immunoinformatics
2
immunology
2
heterogeneity
2
RIPSeq
2
heterogeneous-populations
1
differential-gene-expression
1
multinomial-dirichlet-prior
1
differential-analysis
1
bcr-repertoire
1
nucleosome-positioning
1