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bioconductor.org "Clustering" keyword

View the packages on the bioconductor.org package registry that are tagged with the "Clustering" keyword.

crumblr 1.0.0
Count ratio uncertainty modeling base linear regression
1 version - Latest release: 3 months ago - 1.15 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
PICS 2.51.0
Probabilistic inference of ChIP-seq
5 versions - Latest release: 2 months ago - 1 dependent package - 47.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
scBubbletree 1.10.0
Quantitative visual exploration of scRNA-seq data
5 versions - Latest release: 2 months ago - 5.44 thousand downloads total - 7 stars on GitHub - 1 maintainer
BioCor 1.32.0
Functional similarities
5 versions - Latest release: 2 months ago - 18.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
MOGAMUN 1.18.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
5 versions - Latest release: 2 months ago - 7.53 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R
23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
rrvgo 1.20.0
Reduce + Visualize GO
7 versions - Latest release: 3 months ago - 30.3 thousand downloads total - 30 stars on GitHub - 1 maintainer
eiR 1.48.0
Accelerated similarity searching of small molecules
5 versions - Latest release: 3 months ago - 20.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
DESeq2 1.48.1
Differential gene expression analysis based on the negative binomial distribution
7 versions - Latest release: 2 months ago - 146 dependent packages - 3.33 million downloads total - 330 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.64.1
Linear Models for Microarray and Omics Data
14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.16.0
A universal enrichment tool for interpreting omics data
14 versions - Latest release: 3 months ago - 59 dependent packages - 1.92 million downloads total - 1 maintainer
Top 3.3% on bioconductor.org
destiny 3.22.0
Creates diffusion maps
5 versions - Latest release: 2 months ago - 4 dependent packages - 152 thousand downloads total - 86 stars on GitHub - 1 maintainer
Top 5.1% on bioconductor.org
M3C 1.30.0
Monte Carlo Reference-based Consensus Clustering
5 versions - Latest release: 3 months ago - 77.6 thousand downloads total - 1 maintainer
miRSM 2.4.0
Inferring miRNA sponge modules in heterogeneous data
6 versions - Latest release: 3 months ago - 10.2 thousand downloads total - 4 stars on GitHub - 1 maintainer
CDI 1.6.0
Clustering Deviation Index (CDI)
5 versions - Latest release: 3 months ago - 4.15 thousand downloads total - 5 stars on GitHub - 1 maintainer
SomaticSignatures 2.44.0
Somatic Signatures
5 versions - Latest release: 3 months ago - 1 dependent package - 51.1 thousand downloads total - 22 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 3.16.3
an R package for visualization of tree and annotation data
8 versions - Latest release: 9 days ago - 28 dependent packages - 1.69 million downloads total - 1 maintainer
GraphPAC 1.50.0
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
5 versions - Latest release: 3 months ago - 1 dependent package - 24 thousand downloads total - 1 maintainer
ELViS 1.0.0
An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Rea...
1 version - Latest release: 3 months ago - 1.18 thousand downloads total - 0 stars on GitHub - 1 maintainer
simplifyEnrichment 2.2.0
Simplify Functional Enrichment Results
6 versions - Latest release: 3 months ago - 4 dependent packages - 49.4 thousand downloads total - 115 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
bluster 1.18.0
Clustering Algorithms for Bioconductor
5 versions - Latest release: 2 months ago - 12 dependent packages - 384 thousand downloads total - 1 maintainer
NetPathMiner 1.44.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization
5 versions - Latest release: 3 months ago - 23.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
poem 1.0.1
POpulation-based Evaluation Metrics
2 versions - Latest release: 2 months ago - 1.08 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 3.4% on bioconductor.org
FlowSOM 2.16.0
Using self-organizing maps for visualization and interpretation of cytometry data
5 versions - Latest release: 2 months ago - 3 dependent packages - 154 thousand downloads total - 1 maintainer
QUBIC 1.36.0
An R package for qualitative biclustering in support of gene co-expression analyses
5 versions - Latest release: 3 months ago - 2 dependent packages - 30.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
ConsensusClusterPlus 1.72.0
ConsensusClusterPlus
5 versions - Latest release: 3 months ago - 7 dependent packages - 371 thousand downloads total - 1 maintainer
selectKSigs 1.20.0
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
5 versions - Latest release: 2 months ago - 7.99 thousand downloads total - 0 stars on GitHub - 1 maintainer
censcyt 1.16.0
Differential abundance analysis with a right censored covariate in high-dimensional cytometry
5 versions - Latest release: 2 months ago - 6.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
ChemmineR 3.60.0
Cheminformatics Toolkit for R
5 versions - Latest release: 2 months ago - 8 dependent packages - 503 thousand downloads total - 16 stars on GitHub - 1 maintainer
GeDi 1.4.0
Defining and visualizing the distances between different genesets
4 versions - Latest release: 3 months ago - 3.29 thousand downloads total - 1 stars on GitHub - 1 maintainer
tidybulk 1.20.0
Brings transcriptomics to the tidyverse
7 versions - Latest release: 2 months ago - 1 dependent package - 17.8 thousand downloads total - 173 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
BiocNeighbors 2.2.0
Nearest Neighbor Detection for Bioconductor Packages
7 versions - Latest release: 2 months ago - 18 dependent packages - 890 thousand downloads total - 1 maintainer
seqArchR 1.12.0
Identify Different Architectures of Sequence Elements
5 versions - Latest release: 3 months ago - 1 dependent package - 6.34 thousand downloads total - 1 stars on GitHub - 1 maintainer
immunoClust 1.40.0
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
5 versions - Latest release: 2 months ago - 18.2 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
phyloseq 1.52.0
Handling and analysis of high-throughput microbiome census data
5 versions - Latest release: 2 months ago - 23 dependent packages - 831 thousand downloads total - 1 maintainer
SingleCellSignalR 1.20.0
Cell Signalling Using Single Cell RNAseq Data Analysis
5 versions - Latest release: 3 months ago - 3 dependent packages - 18.8 thousand downloads total - 1 maintainer
RIVER 1.32.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)
5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
ClustIRR 1.6.0
Clustering of immune receptor repertoires
4 versions - Latest release: 2 months ago - 4.31 thousand downloads total - 3 stars on GitHub - 1 maintainer
HiCDOC 1.10.1
A/B compartment detection and differential analysis
7 versions - Latest release: 2 months ago - 6.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
DECIPHER 3.4.0
Tools for curating, analyzing, and manipulating biological sequences
5 versions - Latest release: 2 months ago - 7 dependent packages - 272 thousand downloads total - 1 maintainer
MAPFX 1.4.0
MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massivel...
3 versions - Latest release: 2 months ago - 3.17 thousand downloads total - 1 stars on GitHub - 1 maintainer
multiWGCNA 1.6.0
multiWGCNA
4 versions - Latest release: 3 months ago - 5.35 thousand downloads total - 1 maintainer
GOexpress 1.42.0
Visualise microarray and RNAseq data using gene ontology annotations
5 versions - Latest release: 2 months ago - 1 dependent package - 29.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
DirichletMultinomial 1.50.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
5 versions - Latest release: 3 months ago - 5 dependent packages - 396 thousand downloads total - 11 stars on GitHub - 1 maintainer
PING 2.51.0
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
5 versions - Latest release: 3 months ago - 28.5 thousand downloads total - 1 maintainer
concordexR 1.8.0
Identify Spatial Homogeneous Regions with concordex
5 versions - Latest release: 3 months ago - 5.26 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
tradeSeq 1.22.0
trajectory-based differential expression analysis for sequencing data
5 versions - Latest release: 2 months ago - 45.1 thousand downloads total - 265 stars on GitHub - 1 maintainer
CelliD 1.16.0
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
6 versions - Latest release: 2 months ago - 18.1 thousand downloads total - 1 maintainer
iSEEfier 1.4.0
Streamlining the creation of initial states for starting an iSEE instance
3 versions - Latest release: 2 months ago - 3.29 thousand downloads total - 0 stars on GitHub - 1 maintainer
GOpro 1.34.0
Find the most characteristic gene ontology terms for groups of human genes
5 versions - Latest release: 3 months ago - 20.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
smoothclust 1.4.0
smoothclust
5 versions - Latest release: 2 months ago - 3.54 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
kebabs 1.42.0
Kernel-Based Analysis of Biological Sequences
5 versions - Latest release: 2 months ago - 2 dependent packages - 38.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.4% on bioconductor.org
Mfuzz 2.68.0
Soft clustering of omics time series data
5 versions - Latest release: 3 months ago - 5 dependent packages - 153 thousand downloads total - 1 maintainer
FEAST 1.16.0
FEAture SelcTion (FEAST) for Single-cell clustering
5 versions - Latest release: 3 months ago - 9.81 thousand downloads total - 9 stars on GitHub - 1 maintainer
pipeComp 1.18.0
pipeComp pipeline benchmarking framework
5 versions - Latest release: 3 months ago - 7.97 thousand downloads total - 1 maintainer
MAGAR 1.16.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
5 versions - Latest release: 2 months ago - 8.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
ChromSCape 1.17.0
Analysis of single-cell epigenomics datasets with a Shiny App
5 versions - Latest release: 2 months ago - 7.92 thousand downloads total - 14 stars on GitHub - 1 maintainer
ClusterSignificance 1.36.0
The ClusterSignificance package provides tools to assess if class clusters in dimensionality redu...
5 versions - Latest release: 2 months ago - 15.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
MultiRNAflow 1.6.0
An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
4 versions - Latest release: 3 months ago - 4.66 thousand downloads total - 0 stars on GitHub - 1 maintainer
BayesSpace 1.18.3
Clustering and Resolution Enhancement of Spatial Transcriptomes
7 versions - Latest release: 10 days ago - 1 dependent package - 21.9 thousand downloads total - 145 stars on GitHub - 1 maintainer
SpectralTAD 1.24.0
SpectralTAD: Hierarchical TAD detection using spectral clustering
5 versions - Latest release: 2 months ago - 1 dependent package - 11.9 thousand downloads total - 10 stars on GitHub - 1 maintainer
GenomicSuperSignature 1.16.1
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
6 versions - Latest release: 2 months ago - 7.45 thousand downloads total - 12 stars on GitHub - 1 maintainer
protGear 1.12.0
Protein Micro Array Data Management and Interactive Visualization
5 versions - Latest release: 3 months ago - 7.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
netboost 2.16.0
Network Analysis Supported by Boosting
5 versions - Latest release: 3 months ago - 8.54 thousand downloads total - 1 maintainer
Cardinal 3.10.0
A mass spectrometry imaging toolbox for statistical analysis
10 versions - Latest release: 3 months ago - 34.9 thousand downloads total - 1 maintainer
GSgalgoR 1.18.0
An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatur...
5 versions - Latest release: 3 months ago - 7.81 thousand downloads total - 15 stars on GitHub - 1 maintainer
ClusterJudge 1.30.0
Judging Quality of Clustering Methods using Mutual Information
5 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 1 maintainer
Banksy 1.4.0
Spatial transcriptomic clustering
3 versions - Latest release: 3 months ago - 8.14 thousand downloads total - 111 stars on GitHub - 1 maintainer
cicero 1.26.0
Predict cis-co-accessibility from single-cell chromatin accessibility data
5 versions - Latest release: 3 months ago - 30.2 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
SingleR 2.10.0
Reference-Based Single-Cell RNA-Seq Annotation
6 versions - Latest release: 3 months ago - 5 dependent packages - 289 thousand downloads total - 191 stars on GitHub - 1 maintainer
GWENA 1.18.0
Pipeline for augmented co-expression analysis
5 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
squallms 1.2.0
Speedy quality assurance via lasso labeling for LC-MS data
2 versions - Latest release: 3 months ago - 2.01 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.9% on bioconductor.org
CATALYST 1.32.0
Cytometry dATa anALYSis Tools
8 versions - Latest release: 3 months ago - 5 dependent packages - 63.4 thousand downloads total - 68 stars on GitHub - 1 maintainer
systemPipeTools 1.16.0
Tools for data visualization
5 versions - Latest release: 3 months ago - 6.35 thousand downloads total - 1 maintainer
cyanoFilter 1.16.0
Phytoplankton Population Identification using Cell Pigmentation and/or Complexity
5 versions - Latest release: 3 months ago - 8.48 thousand downloads total - 0 stars on GitHub - 1 maintainer
iPAC 1.52.0
Identification of Protein Amino acid Clustering
5 versions - Latest release: 3 months ago - 3 dependent packages - 26.6 thousand downloads total - 1 maintainer
scDiagnostics 1.2.0
Cell type annotation diagnostics
2 versions - Latest release: 3 months ago - 1.94 thousand downloads total - 9 stars on GitHub - 1 maintainer
cola 2.14.0
A Framework for Consensus Partitioning
5 versions - Latest release: 3 months ago - 2 dependent packages - 15 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.1% on bioconductor.org
treeio 1.32.0
Base Classes and Functions for Phylogenetic Tree Input and Output
5 versions - Latest release: 3 months ago - 7 dependent packages - 1.4 million downloads total - 1 maintainer
MPAC 1.2.0
Multi-omic Pathway Analysis of Cells
2 versions - Latest release: 3 months ago - 2.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
ChemmineOB 1.46.0
R interface to a subset of OpenBabel functionalities
5 versions - Latest release: 3 months ago - 2 dependent packages - 231 thousand downloads total - 11 stars on GitHub - 1 maintainer
rScudo 1.24.0
Signature-based Clustering for Diagnostic Purposes
6 versions - Latest release: 3 months ago - 9.68 thousand downloads total - 4 stars on GitHub - 1 maintainer
tanggle 1.14.0
Visualization of Phylogenetic Networks
5 versions - Latest release: 3 months ago - 6.53 thousand downloads total - 10 stars on GitHub - 1 maintainer
scDotPlot 1.2.0
Cluster a Single-cell RNA-seq Dot Plot
2 versions - Latest release: 2 months ago - 2.54 thousand downloads total - 7 stars on GitHub - 1 maintainer
CHETAH 1.24.0
Fast and accurate scRNA-seq cell type identification
5 versions - Latest release: 3 months ago - 1 dependent package - 13.9 thousand downloads total - 40 stars on GitHub - 1 maintainer
tidySummarizedExperiment 1.18.1
Brings SummarizedExperiment to the Tidyverse
6 versions - Latest release: 2 months ago - 5 dependent packages - 18.1 thousand downloads total - 26 stars on GitHub - 1 maintainer
tidySingleCellExperiment 1.18.1
Brings SingleCellExperiment to the Tidyverse
6 versions - Latest release: 2 months ago - 4 dependent packages - 14.5 thousand downloads total - 36 stars on GitHub - 1 maintainer
ILoReg 1.18.0
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
6 versions - Latest release: 3 months ago - 7.46 thousand downloads total - 5 stars on GitHub - 1 maintainer
MOMA 1.20.0
Multi Omic Master Regulator Analysis
5 versions - Latest release: 3 months ago - 8.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
GARS 1.28.0
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional...
5 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 1 maintainer
vsclust 1.10.0
Feature-based variance-sensitive quantitative clustering
5 versions - Latest release: 3 months ago - 5.01 thousand downloads total - 1 maintainer
scrapper 1.2.1
Bindings to C++ Libraries for Single-Cell Analysis
5 versions - Latest release: about 2 months ago - 4.19 thousand downloads total - 1 maintainer
Rigraphlib 1.0.0
igraph library as an R package
1 version - Latest release: 3 months ago - 2.91 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
iSEE 2.20.0
Interactive SummarizedExperiment Explorer
5 versions - Latest release: 2 months ago - 8 dependent packages - 46.3 thousand downloads total - 228 stars on GitHub - 1 maintainer
survClust 1.2.0
Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning
2 versions - Latest release: 3 months ago - 2.35 thousand downloads total - 16 stars on GitHub - 1 maintainer
hapFabia 1.50.0
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rar...
5 versions - Latest release: 3 months ago - 26.7 thousand downloads total - 1 maintainer
bandle 1.12.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
5 versions - Latest release: 2 months ago - 6.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
ANF 1.30.0
Affinity Network Fusion for Complex Patient Clustering
6 versions - Latest release: 3 months ago - 14.9 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
scran 1.36.0
Methods for Single-Cell RNA-Seq Data Analysis
7 versions - Latest release: 3 months ago - 62 dependent packages - 510 thousand downloads total - 41 stars on GitHub - 1 maintainer
ccfindR 1.28.0
Cancer Clone Finder
5 versions - Latest release: 3 months ago - 1 dependent package - 16.4 thousand downloads total - 1 maintainer
Related Keywords
Software 309 GeneExpression 118 Sequencing 95 Visualization 94 ImmunoOncology 84 RNASeq 79 SingleCell 79 DifferentialExpression 71 Transcriptomics 61 Classification 60 MultipleComparison 50 Microarray 47 Normalization 40 Transcription 38 DataImport 37 QualityControl 35 GeneSetEnrichment 31 Preprocessing 31 DimensionReduction 31 StatisticalMethod 30 GraphAndNetwork 29 Proteomics 29 Network 29 BiomedicalInformatics 28 FeatureExtraction 28 Bayesian 27 Regression 26 CellBasedAssays 23 FlowCytometry 23 Annotation 22 SystemsBiology 22 CellBiology 21 Pathways 20 Genetics 20 GO 19 TimeCourse 19 DataRepresentation 19 PrincipalComponent 19 Infrastructure 16 BatchEffect 16 Epigenetics 16 r 15 FunctionalGenomics 15 Metabolomics 13 Coverage 13 Spatial 12 ChIPSeq 11 KEGG 11 mRNAMicroarray 10 GeneRegulation 10 GUI 10 GeneticVariability 10 Survival 10 SNP 9 bioconductor 9 Microbiome 8 bioinformatics 8 MassSpectrometry 8 DNAMethylation 8 ReportWriting 7 Alignment 7 ATACSeq 7 NetworkInference 7 OneChannel 7 DNASeq 7 Metagenomics 7 DifferentialSplicing 7 AlternativeSplicing 7 clustering 7 SomaticMutation 6 GenomicVariation 6 ShinyApps 6 NetworkEnrichment 6 single-cell 6 CopyNumberVariation 6 transcriptomics 6 Cheminformatics 6 TwoChannel 6 ExperimentalDesign 6 DifferentialMethylation 5 Pharmacogenomics 5 HiC 5 Pharmacogenetics 5 Phylogenetics 5 AssayDomain 5 human-cell-atlas 5 GenePrediction 5 bioconductor-package 5 ExonArray 5 r-package 4 GeneTarget 4 tidyverse 4 ProprietaryPlatforms 4 MicroRNAArray 4 MethylSeq 4 MicrotitrePlateAssay 4 FunctionalPrediction 3 BiologicalQuestion 3 shiny 3 single-cell-rna-seq 3