Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Bayesian" keyword
gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...6 versions - Latest release: 6 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
bacon 1.30.0
Controlling bias and inflation in association studies using the empirical null distribution3 versions - Latest release: 6 months ago - 16.9 thousand downloads total - 1 maintainer
Clomial 1.38.0
Infers clonal composition of a tumor3 versions - Latest release: 6 months ago - 16.4 thousand downloads total - 1 maintainer
INTACT 1.2.0
Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis3 versions - Latest release: 6 months ago - 1.24 thousand downloads total - 8 stars on GitHub - 1 maintainer
graper 1.18.0
Adaptive penalization in high-dimensional regression and classification with external covariates ...3 versions - Latest release: 6 months ago - 5.5 thousand downloads total - 1 maintainer
tigre 1.56.0
Transcription factor Inference through Gaussian process Reconstruction of Expression3 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
BaalChIP 1.28.0
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes3 versions - Latest release: 6 months ago - 11.7 thousand downloads total - 1 maintainer
scDD 1.26.0
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions3 versions - Latest release: 6 months ago - 1 dependent package - 19.2 thousand downloads total - 32 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
baySeq 2.38.0
Empirical Bayesian analysis of patterns of differential expression in count data3 versions - Latest release: 13 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
R3CPET 1.34.1
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process4 versions - Latest release: 4 months ago - 12.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
HiLDA 1.16.0
Conducting statistical inference on comparing the mutational exposures of mutational signatures b...3 versions - Latest release: 6 months ago - 1 dependent package - 5.69 thousand downloads total - 3 stars on GitHub - 1 maintainer
sparseDOSSA 1.26.0
Sparse Data Observations for Simulating Synthetic Abundance3 versions - Latest release: 6 months ago - 8.14 thousand downloads total - 1 maintainer
GmicR 1.16.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...3 versions - Latest release: 6 months ago - 5.69 thousand downloads total - 1 maintainer
EBcoexpress 1.46.0
EBcoexpress for Differential Co-Expression Analysis3 versions - Latest release: 6 months ago - 1 dependent package - 23.5 thousand downloads total - 1 maintainer
omicplotR 1.22.0
Visual Exploration of Omic Datasets Using a Shiny App3 versions - Latest release: 6 months ago - 8.13 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets3 versions - Latest release: 6 months ago - 3 dependent packages - 29.2 thousand downloads total - 4 maintainers
CSSP 1.40.0 removed
ChIP-Seq Statistical Power2 versions - Latest release: 6 months ago - 17.8 thousand downloads total
KBoost 1.10.0
Inference of gene regulatory networks from gene expression data3 versions - Latest release: 6 months ago - 2.94 thousand downloads total - 4 stars on GitHub - 1 maintainer
phenopath 1.26.0
Genomic trajectories with heterogeneous genetic and environmental backgrounds3 versions - Latest release: 6 months ago - 1 dependent package - 11 thousand downloads total - 1 maintainer
mfa 1.24.0
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations3 versions - Latest release: 6 months ago - 1 dependent package - 10.8 thousand downloads total - 1 maintainer
RJMCMCNucleosomes 1.26.0
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-rea...3 versions - Latest release: 6 months ago - 9.13 thousand downloads total - 0 stars on GitHub - 1 maintainer
hummingbird 1.12.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions3 versions - Latest release: 6 months ago - 3.39 thousand downloads total - 1 maintainer
BPRMeth 1.28.0
Model higher-order methylation profiles3 versions - Latest release: 6 months ago - 1 dependent package - 11.9 thousand downloads total - 1 maintainer
MADSEQ 1.28.0
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data3 versions - Latest release: 6 months ago - 9.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
BDMMAcorrect 1.20.0
Meta-analysis for the metagenomic read counts data from different cohorts3 versions - Latest release: 6 months ago - 6.33 thousand downloads total - 1 maintainer
scMET 1.4.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity3 versions - Latest release: 6 months ago - 1.73 thousand downloads total - 18 stars on GitHub - 1 maintainer
ccfindR 1.22.0
Cancer Clone Finder3 versions - Latest release: 6 months ago - 1 dependent package - 11.4 thousand downloads total - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 6 months ago - 7.55 thousand downloads total - 1 maintainer
ATACCoGAPS 1.4.0
Analysis Tools for scATACseq Data with CoGAPS3 versions - Latest release: 6 months ago - 1.55 thousand downloads total - 4 stars on GitHub - 1 maintainer
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: 6 months ago - 7.94 thousand downloads total - 1 maintainer
BUMHMM 1.26.0
Computational pipeline for computing probability of modification from structure probing experimen...3 versions - Latest release: 6 months ago - 9.56 thousand downloads total - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
GRENITS 1.54.0
Gene Regulatory Network Inference Using Time Series3 versions - Latest release: 6 months ago - 23.6 thousand downloads total - 1 maintainer
normr 1.28.0
Normalization and difference calling in ChIP-seq data3 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
rRDP 1.36.0
Interface to the RDP Classifier3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
bandle 1.6.0
An R package for the Bayesian analysis of differential subcellular localisation experiments3 versions - Latest release: 6 months ago - 2.26 thousand downloads total - 5 stars on GitHub - 1 maintainer
ternarynet 1.46.0
Ternary Network Estimation3 versions - Latest release: 6 months ago - 19.4 thousand downloads total - 1 maintainer
BayesKnockdown 1.28.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data3 versions - Latest release: 6 months ago - 9.92 thousand downloads total - 1 maintainer
TRONCO 2.34.0
TRONCO, an R package for TRanslational ONCOlogy3 versions - Latest release: 6 months ago - 16.6 thousand downloads total - 1 maintainer
BAGS 2.42.0
A Bayesian Approach for Geneset Selection3 versions - Latest release: 6 months ago - 19.4 thousand downloads total - 1 maintainer
scDDboost 1.4.0
A compositional model to assess expression changes from single-cell rna-seq data3 versions - Latest release: 6 months ago - 1.63 thousand downloads total - 0 stars on GitHub - 1 maintainer
OpenStats 1.14.0
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phen...3 versions - Latest release: 6 months ago - 4.39 thousand downloads total - 1 maintainer
BG2 1.2.0
Performs Bayesian GWAS analysis for non-Gaussian data using BG23 versions - Latest release: 6 months ago - 1.3 thousand downloads total - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
metaseqR2 1.14.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...3 versions - Latest release: 6 months ago - 5.12 thousand downloads total - 1 maintainer
banocc 1.26.0
Bayesian ANalysis Of Compositional Covariance3 versions - Latest release: 6 months ago - 9.88 thousand downloads total - 2 maintainers
beer 1.6.0
Bayesian Enrichment Estimation in R3 versions - Latest release: 6 months ago - 2.33 thousand downloads total - 5 stars on GitHub - 1 maintainer
IntOMICS 1.2.0
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: 6 months ago - 1.05 thousand downloads total - 0 stars on GitHub - 1 maintainer
PROPS 1.24.0
PRObabilistic Pathway Score (PROPS)3 versions - Latest release: 6 months ago - 7.6 thousand downloads total - 1 maintainer
STdeconvolve 1.6.0
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data3 versions - Latest release: 6 months ago - 3.66 thousand downloads total - 1 maintainer
GWAS.BAYES 1.12.0
Bayesian analysis of Gaussian GWAS data3 versions - Latest release: 6 months ago - 3.6 thousand downloads total - 1 maintainer
BUScorrect 1.20.0
Batch Effects Correction with Unknown Subtypes3 versions - Latest release: 6 months ago - 6.23 thousand downloads total - 1 maintainer
EBSeqHMM 1.35.0
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 1 maintainer
ASSIGN 1.38.0
Adaptive Signature Selection and InteGratioN (ASSIGN)3 versions - Latest release: 6 months ago - 1 dependent package - 19.8 thousand downloads total - 2 stars on GitHub - 4 maintainers
wavClusteR 2.36.0
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data3 versions - Latest release: 6 months ago - 16.8 thousand downloads total - 1 maintainer
IsoBayes 1.2.0
IsoBayes: Single Isoform protein inference Method via Bayesian Analyses3 versions - Latest release: 15 days ago - 832 downloads total - 5 stars on GitHub - 1 maintainer
gemini 1.16.0
GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens3 versions - Latest release: 6 months ago - 4.81 thousand downloads total - 15 stars on GitHub - 1 maintainer
BUSseq 1.8.0
Batch Effect Correction with Unknow Subtypes for scRNA-seq data3 versions - Latest release: 6 months ago - 2.52 thousand downloads total - 0 stars on GitHub - 1 maintainer
NormalyzerDE 1.20.0
Evaluation of normalization methods and calculation of differential expression analysis statistics3 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
4 versions - Latest release: 20 days ago - 146 dependent packages - 2.77 million downloads total - 328 stars on GitHub - 1 maintainer
DESeq2 1.44.0
Differential gene expression analysis based on the negative binomial distribution4 versions - Latest release: 20 days ago - 146 dependent packages - 2.77 million downloads total - 328 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 19 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 19 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
retrofit 1.4.0
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics3 versions - Latest release: 20 days ago - 1.07 thousand downloads total - 4 stars on GitHub - 1 maintainer
IgGeneUsage 1.18.0
Differential gene usage in immune repertoires3 versions - Latest release: 8 days ago - 4.83 thousand downloads total - 6 stars on GitHub - 1 maintainer
DEqMS 1.22.0
a tool to perform statistical analysis of differential protein expression for quantitative proteo...3 versions - Latest release: 8 days ago - 13.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
BASiCStan 1.6.0
Stan implementation of BASiCS3 versions - Latest release: 8 days ago - 1.67 thousand downloads total - 0 stars on GitHub - 1 maintainer
BANDITS 1.20.0
BANDITS: Bayesian ANalysis of DIfferenTial Splicing4 versions - Latest release: 9 days ago - 1 dependent package - 7.51 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 11 dependent packages - 252 thousand downloads total - 1 maintainer
apeglm 1.26.0
Approximate posterior estimation for GLM coefficients3 versions - Latest release: 13 days ago - 11 dependent packages - 252 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
ALDEx2 1.36.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account3 versions - Latest release: 13 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
3 versions - Latest release: 13 days ago - 48.9 thousand downloads total - 1 maintainer
limmaGUI 1.80.0
GUI for limma Package With Two Color Microarrays3 versions - Latest release: 13 days ago - 48.9 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
puma 3.46.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...3 versions - Latest release: 13 days ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
3 versions - Latest release: 13 days ago - 54.1 thousand downloads total - 1 maintainer
scde 2.32.0
Single Cell Differential Expression3 versions - Latest release: 13 days ago - 54.1 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 66 thousand downloads total - 1 maintainer
affylmGUI 1.78.0
GUI for limma Package with Affymetrix Microarrays3 versions - Latest release: 13 days ago - 66 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
5 versions - Latest release: 13 days ago - 2 dependent packages - 32.5 thousand downloads total - 133 stars on GitHub - 1 maintainer
celda 1.20.0
CEllular Latent Dirichlet Allocation5 versions - Latest release: 13 days ago - 2 dependent packages - 32.5 thousand downloads total - 133 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
4 versions - Latest release: 14 days ago - 22.5 thousand downloads total - 271 stars on GitHub - 1 maintainer
MOFA2 1.14.0
Multi-Omics Factor Analysis v24 versions - Latest release: 14 days ago - 22.5 thousand downloads total - 271 stars on GitHub - 1 maintainer
CBNplot 1.4.0
plot bayesian network inferred from gene expression data based on enrichment analysis results4 versions - Latest release: 16 days ago - 2.56 thousand downloads total - 52 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)2 versions - Latest release: 6 months ago - 8.53 thousand downloads total - 10 stars on GitHub - 1 maintainer
proDA 1.16.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data2 versions - Latest release: 7 months ago - 1 dependent package - 11.1 thousand downloads total - 14 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
decontX 1.0.0
Decontamination of single cell genomics data1 version - Latest release: 7 months ago - 1.69 thousand downloads total - 1 maintainer
ctsGE 1.28.0
Clustering of Time Series Gene Expression data2 versions - Latest release: 6 months ago - 10.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing2 versions - Latest release: 6 months ago - 4.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
DMCFB 1.16.1
Differentially Methylated Cytosines via a Bayesian Functional Approach3 versions - Latest release: 3 months ago - 4.61 thousand downloads total - 0 stars on GitHub - 1 maintainer
protGear 1.6.0
Protein Micro Array Data Management and Interactive Visualization2 versions - Latest release: 7 months ago - 1.98 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
2 versions - Latest release: 7 months ago - 19 dependent packages - 579 thousand downloads total - 44 stars on GitHub - 1 maintainer
pcaMethods 1.94.0
A collection of PCA methods2 versions - Latest release: 7 months ago - 19 dependent packages - 579 thousand downloads total - 44 stars on GitHub - 1 maintainer
plasmut 1.0.0
Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic,...1 version - Latest release: 7 months ago - 518 downloads total - 1 maintainer
BASiCS 2.14.0
Bayesian Analysis of Single-Cell Sequencing data2 versions - Latest release: 6 months ago - 2 dependent packages - 16.7 thousand downloads total - 83 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 77.8 thousand downloads total - 502 stars on GitHub - 1 maintainer
infercnv 1.18.1
Infer Copy Number Variation from Single-Cell RNA-Seq Data3 versions - Latest release: 6 months ago - 77.8 thousand downloads total - 502 stars on GitHub - 1 maintainer
DifferentialRegulation 2.0.3
Differentially regulated genes from scRNA-seq data5 versions - Latest release: 3 months ago - 1.91 thousand downloads total - 8 stars on GitHub - 1 maintainer
covEB 1.28.0
Empirical Bayes estimate of block diagonal covariance matrices2 versions - Latest release: 6 months ago - 9.5 thousand downloads total - 1 maintainer
Related Keywords
Software
90
GeneExpression
49
ImmunoOncology
39
Sequencing
38
RNASeq
32
DifferentialExpression
32
Clustering
26
Regression
22
SingleCell
20
MultipleComparison
20
Transcriptomics
18
Transcription
18
Genetics
17
Normalization
16
StatisticalMethod
15
DataImport
14
BatchEffect
14
Microarray
13
Preprocessing
12
TimeCourse
12
QualityControl
11
GeneSetEnrichment
10
GeneRegulation
10
Visualization
10
Coverage
10
Network
10
Proteomics
10
BiomedicalInformatics
10
SystemsBiology
9
Epigenetics
8
AlternativeSplicing
8
NetworkInference
8
FeatureExtraction
8
DifferentialSplicing
8
ChIPSeq
8
mRNAMicroarray
7
GraphAndNetwork
7
Classification
7
CellBiology
7
DNAMethylation
6
FunctionalGenomics
6
OneChannel
6
Microbiome
5
DifferentialMethylation
5
ExonArray
5
ProprietaryPlatforms
5
TwoChannel
5
Pathways
5
Metagenomics
4
GUI
4
DimensionReduction
4
bayesian
4
MicroRNAArray
4
r
4
SomaticMutation
4
Metabolomics
4
HiddenMarkovModel
4
MassSpectrometry
4
CopyNumberVariation
4
SNP
3
bioinformatics
3
GenomeWideAssociation
3
GenomicVariation
3
DNASeq
3
PrincipalComponent
3
GeneticVariability
3
KEGG
3
VariantDetection
2
single-cell
2
AssayDomain
2
heterogeneity
2
bioconductor
2
Spatial
2
GeneTarget
2
Survival
2
limma
2
Alignment
2
GenePrediction
2
SAGE
2
Cheminformatics
2
MethylationArray
2
transcriptomics
2
RIPSeq
2
ExperimentalDesign
2
mofa
1
systemsbiology
1
differential-analysis
1
differential-gene-expression
1
high-throughput-sequencing
1
immune-repertoire
1
immune-repertoire-analysis
1
immune-repertoires
1
immunogenomics
1
immunoglobulin
1
immunoinformatics
1
immunological-bioinformatics
1
immunology
1
tcr-repertoire
1
vdj-recombination
1
ExperimentHubSoftware
1