Biocview "Clustering"

A bioconductor package for high-dimensional exploration of biological network heterogeneity
A bioconductor package for high-dimensional exploration of biological network heterogeneity
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accurate hierarchical clustering for huge data
A collection of gene feature selection and clustering analysis algorithms
Advanced analysis of microbial flow cytometry data
Affinity Network Fusion for Complex Patient Clustering
Affinity Network Fusion for Complex Patient Clustering
A gene recommender algorithm to identify genes coexpressed with a query set of genes
A gene recommender algorithm to identify genes coexpressed with a query set of genes
A mass spectrometry imaging toolbox for statistical analysis
A mass spectrometry imaging toolbox for statistical analysis
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of RNA-Seq Count Data by Using Multiple Corespondence Analysis
Analysis of RNA-Seq Count Data by Using Multiple Corespondence Analysis
Analyze flow cytometric data using gate information
Analyze flow cytometric data using gate information
Analyze flow cytometric data using histogram information
Analyze flow cytometric data using histogram information
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
Annotation-Driven Clustering
Annotation-Driven Clustering
An R package for analysis of case-control studies in genetic epidemiology
An R package for analysis of case-control studies in genetic epidemiology
An R package for flow data clustering
An R package for flow data clustering
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for qualitative biclustering in support of gene co-expression analyses
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
A package for nonlinear dimension reduction with Isomap and LLE.
A package for nonlinear dimension reduction with Isomap and LLE.
Asessing statistical significance in predictive GWA studies
Asessing statistical significance in predictive GWA studies
A Shiny App to accompany clusterExperiment
A Tidy Tool for Phylogenetic Tree Data Manipulation
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Bayesian Hierarchical Clustering
Bayesian Hierarchical Clustering
Biclustering Analysis and Results Exploration
Biclustering Analysis and Results Exploration
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cell OrderiNg by FluorEScence Signal
Cell OrderiNg by FluorEScence Signal
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
chroGPS: visualizing the epigenome
chroGPS: visualizing the epigenome
Classes and Methods for "Class Discovery" with Microarrays or Proteomics
Classes and Methods for "Class Discovery" with Microarrays or Proteomics
Classes and Methods for "Class Prediction" with Microarrays or Proteomics
Classes and Methods for Cross Validation of "Class Prediction" Algorithms
Classes and Methods for Cross Validation of "Class Prediction" Algorithms
Classes and methods for cross validation of "class prediction" with microarrays or proteomics
Classes and methods for multi-omics data integration
Classes and methods for multi-omics data integration
Classes and methods for multi-omics data integration
Classes and Methods for Training and Using Binary Prediction Models
Classes and Methods for Training and Using Binary Prediction Models
Classes and Methods to Use Genetic Algorithms for Feature Selection
Classes and Methods to Use Genetic Algorithms for Feature Selection
Cluster and Tree Conversion.
Cluster and Tree Conversion.
Clustering algorithm for ddPCR data
Clustering algorithm for ddPCR data
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering approach to solve complete Deconvolution problem
Clustering Comparison Package
Clustering Comparison Package
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering for Flow Cytometry
Clustering for Flow Cytometry
Clustering for Flow Cytometry
Clustering of Genomic Regions Analysis Method
Clustering of Genomic Regions Analysis Method
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Cluster Merging for Flow Cytometry Data
Cluster Merging for Flow Cytometry Data
Cluster Merging for Flow Cytometry Data
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Computation of Gene Expression-Based Signatures in Breast Cancer
Computation of Gene Expression-Based Signatures in Breast Cancer
Computation of Gene Expression-Based Signatures in Breast Cancer
Compute cluster stability scores for microarray data
Compute cluster stability scores for microarray data
Compute Mantel Cluster Correlations
Compute Mantel Cluster Correlations
Condition specific detection from expression data
Condition specific detection from expression data
ConsensusClusterPlus
ConsensusClusterPlus
ConsensusClusterPlus
Contrasts in Mixed Effects for EMMIX Model with Random Effects
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Creates diffusion maps
Creates diffusion maps
Creates diffusion maps
cytofkit: an integrated mass cytometry data analysis pipeline
cytofkit: an integrated mass cytometry data analysis pipeline
cytofkit: an integrated mass cytometry data analysis pipeline
cytofkit: an integrated mass cytometry data analysis pipeline
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
deltaGseg
deltaGseg
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting SNPs with interactive effects on a quantitative trait
Detecting SNPs with interactive effects on a quantitative trait
Different distance measures
Different distance measures
Different distance measures
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differential Methylation Analysis with Targeted Minimum Loss-Based Estimates of Variable Importance Measures
Different methods for the integrative analysis multiple omics data
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Display and manipulate heatmaps in clustergrammer.js
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Example experimental data for use with the methyvim package
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Extended project Morpheus with Bioconductor methods
Extended project Morpheus with Bioconductor methods
FABIA: Factor Analysis for Bicluster Acquisition
FABIA: Factor Analysis for Bicluster Acquisition
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Finding the Number of Significant Principal Components
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Fingerprinting for Flow Cytometry
Fingerprinting for Flow Cytometry
Functional Gene Networks derived from biological enrichment analyses
Functional Gene Networks derived from biological enrichment analyses
Functional Network Analysis
Functional Network Analysis
Functional Network Analysis
Functional similarities
Functional similarities
Functional similarities
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to handle cDNA microarray data, including several methods of data analysis
Gene expression-based subtype classification for high-grade serous ovarian cancer
Gene expression-based subtype classification for high-grade serous ovarian cancer
Gene expression-based subtype classification for high-grade serous ovarian cancer
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
gRx Differential Clustering
gRx Differential Clustering
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Hidden Factor Graph Models
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Identification of Mutational Clusters in 3D Protein Space via Simulation.
Identification of Mutational Clusters in 3D Protein Space via Simulation.
Identification of mutational clusters in protein quaternary structures.
Identification of mutational clusters in protein quaternary structures.
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
Identification of Protein Amino acid Clustering
Identification of Protein Amino acid Clustering
Identifies cell population in flow cytometry data.
Identifies cell population in flow cytometry data.
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Infers biological signatures from gene expression data
Infers biological signatures from gene expression data
Infers clonal composition of a tumor
Infers clonal composition of a tumor
Integrative clustering of multi-type genomic data
Integrative clustering of multi-type genomic data
interactive SingleCell/Summarized Experiment Explorer
Iterative Binary Biclustering of Genesets
Iterative Binary Biclustering of Genesets
Iterative Clustering
Iterative Clustering
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
Judging Quality of Clustering Methods using Mutual Information
Judging Quality of Clustering Methods using Mutual Information
Judging Quality of Clustering Methods using Mutual Information
Kernel-Based Analysis Of Biological Sequences
Kernel-Based Analysis Of Biological Sequences
LEA: an R package for Landscape and Ecological Association Studies
LEA: an R package for Landscape and Ecological Association Studies
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Linear Models for Microarray Data
Linear Models for Microarray Data
Machine learning interface for RNA-Seq data
Machine learning interface for RNA-Seq data
Machine Learning Interface for RNA-Seq Data
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Matching and meta-clustering in flow cytometry
Matching and meta-clustering in flow cytometry
merging of phenotype information from different cytometric profiles
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH(Medical Subject Headings) Semantic Similarity Measures
MeSH(Medical Subject Headings) Semantic Similarity Measures
MetaCyto: A package for meta-analysis of cytometry data
MetaCyto: A package for meta-analysis of cytometry data
Methods for Continuous Flow Cytometry
Methods for visualization and statistics on DNA methylation data
Methods for visualization and statistics on DNA methylation data
Microbial Community Analysis GUI
Microbial Community Analysis GUI
Microbial Comparative Genomics in R
Microbial Comparative Genomics in R
Microbial Comparative Genomics in R
Microbiome Analytics
Microbiome Analytics
Mirsynergy
Mirsynergy
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Model based analysis for paired-end data
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Monte Carlo Consensus Clustering
Monte Carlo Consensus Clustering
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Multiple co-inertia analysis of omics datasets
Multiple co-inertia analysis of omics datasets
Multiple co-inertia analysis of omics datasets
Multiple omics data integrative clustering and gene set analysis
Multiple omics data integrative clustering and gene set analysis
Multiple omics data integrative clustering and gene set analysis
Multivariate analysis of microarray data using ADE4
Multivariate analysis of microarray data using ADE4
Multivariate Correlation Estimator and Statistical Inference Procedures.
Multivariate Correlation Estimator and Statistical Inference Procedures.
Murine Palate miRNA Expression Analysis
Murine Palate miRNA Expression Analysis
Mutation Order Prediction
NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner for Biological Network Construction, Path Mining and Visualization
Non-parametric Flow Cytometry Data Gating
Non-parametric Flow Cytometry Data Gating
OnASSIs Ontology Annotation and Semantic SImilarity software
OnASSIs Ontology Annotation and Semantic SImilarity software
OnASSIs Ontology Annotation and Semantic SImilarity software
Permutation-Based Confidence for Molecular Classification
Permutation-Based Confidence for Molecular Classification
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-seq
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Protein Profiling
Protein Profiling
Qualitative biclustering algorithm for expression data analysis in R
Qualitative biclustering algorithm for expression data analysis in R
RBioinf
RBioinf
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
R interface to a subset of OpenBabel functionalities
R interface to a subset of OpenBabel functionalities
R interface to a subset of OpenBabel functionalities
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
runibic: row-based biclustering algorithm for analysis of gene expression data in R
Run metabarcoding alalyses for multiple amplicons
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
Sequential Flow Cytometry Data Gating
Sequential Flow Cytometry Data Gating
Sequential Flow Cytometry Data Gating
Sequential Flow Cytometry Data Gating
SigFuge
SigFuge
SigFuge
Similarity measures for chemical compounds
Similarity measures for chemical compounds
SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Soft clustering of time series gene expression data
Soft clustering of time series gene expression data
Somatic Signatures
Somatic Signatures
Somatic Signatures
SPADE -- An analysis and visualization tool for Flow Cytometry
SPADE -- An analysis and visualization tool for Flow Cytometry
SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results
Spatial Analysis of Network Associations
Spatial Analysis of Network Associations
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical Analysis of the GeneChip
Statistical Analysis of the GeneChip
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
Targeted Variable Importance for Differential Methylation Analysis
The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data
The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data
The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data
Threshing and Reaping for Principal Components
Time course sequencing data analysis
Time course sequencing data analysis
Time course sequencing data analysis
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Tools for analyzing Micro Array experiments
Tools for analyzing Micro Array experiments
Tools for curating, analyzing, and manipulating biological sequences
Tools for curating, analyzing, and manipulating biological sequences
Tools for microbiome analysis
Tools for ordering single-cell sequencing
Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.
Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
Two-Tier Mapper: a clustering tool based on topological data analysis
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
Using self-organizing maps for visualization and interpretation of cytometry data
Using self-organizing maps for visualization and interpretation of cytometry data
Using self-organizing maps for visualization and interpretation of cytometry data
Using self-organizing maps for visualization and interpretation of cytometry data
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Word cloud summaries of GO enrichment analysis
Word cloud summaries of GO enrichment analysis
Word cloud summaries of GO enrichment analysis
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis