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
Accurate hierarchical clustering for huge data
A collection of tools for imaging MS data processing
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data
Advanced analysis of microbial flow cytometry data
A Fast Scalable and Flexible Non Negative Matrix Factorization Method
Affinity Network Fusion for Complex Patient Clustering
Affinity Network Fusion for Complex Patient Clustering
A Framework for Consensus Partitioning
A Framework for Consensus Partitioning
A gene recommender algorithm to identify genes coexpressed with a query set of genes
A lecture on sequence count data
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 for short time-series data
Analysis for short time-series data
Analysis for short time-series 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 using Multiple Corespondence Analysis
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analyze flow cytometric data using gate 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 small RNA-seq count data
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
Annotation-Driven Clustering
An R package for analysis of case-control studies in genetic epidemiology
An R package for flow data clustering
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation 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
A Shiny App to accompany clusterExperiment
Association analysis of CNVs and imputed SNPs incorporating uncertainty
A time series clustering package combining slope and Frechet distances
A time series clustering package combining slope and Frechet distances
A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
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
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
Batch Effects Correction with Unknown Subtypes
Batch Effects Correction with Unknown Subtypes
Bayesian clustering and imputationa of single cell methylomes
Bayesian clustering and imputationa of single cell methylomes
Bayesian Hierarchical Clustering
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
Biclustering Analysis and Results Exploration
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Build Annotation From Online Database
Cancer Clone Finder
Cancer Clone Finder
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
CB2: A cluster-based approach for distinguishing cells from background barcodes in 10x Genomics data
Cell OrderiNg by FluorEScence Signal
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell Signalling Using Single Cell RNAseq Data Analysis
CEllular Latent Dirichlet Allocation
CEllular Latent Dirichlet Allocation
CEllular Latent Dirichlet Allocation
CHARGE: CHromosome Assessment in R from Gene Expression data
CHARGE: CHromosome Assessment in R from Gene Expression data
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
chroGPS2: Generation, visualization and differential analysis of epigenome maps
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 analysis of Spatial Transcriptomics data
Cluster analysis of Spatial Transcriptomics data
Cluster and Tree Conversion.
Clustering algorithm for ddPCR data
Clustering algorithm for ddPCR data
Clustering algorithm for ddPCR data
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Clustering and Visualizing Binary Matrices
Clustering and Visualizing Distance Matrices
Clustering and Visualizing Distance Matrices
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, 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 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 MS2 Spectra for Metabolite Identification
Clustering of MS2 Spectra for Metabolite Identification
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
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
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 Gene Expression-Based Signatures in Breast Cancer
Computation of Gene Expression-Based Signatures in Breast Cancer
Compute cluster stability scores for microarray data
Compute Mantel Cluster Correlations
Condition Comparison in scRNA-seq Data
Condition Comparison in scRNA-seq Data
Condition specific detection from expression data
ConsensusClusterPlus
ConsensusClusterPlus
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Creates and uses physio spaces as a dimension reduction mapping
Creates diffusion maps
Creates diffusion maps
cytofast - A quick visualization and analysis tool for CyTOF data
cytofast - A quick visualization and analysis tool for CyTOF data
cytofkit: an integrated mass cytometry data analysis pipeline
cytofkit: an integrated mass cytometry data analysis pipeline
cytofkit: an integrated mass cytometry data analysis pipeline
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
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 hidden batch factors through data adaptive adjustment for biological effects
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
dgeAnalysis
Different distance measures
Different distance measures
Differential Analyis of Hi-C Data
Differential Analysis of Hi-C Data
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential Epigenetic Coregulation Test
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Different methods for the integrative analysis multiple omics data
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Display and manipulate heatmaps in clustergrammer.js
Dual redundant reference sequencing
Empirical Analysis of Digital Gene Expression Data in R
Evaluation of Bioinformatics Metrics
Evaluation of Bioinformatics Metrics
Example experimental data for use with the methyvim package
Exploration and Significant Biology on a Gene Set.
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
FABIA: Factor Analysis for Bicluster Acquisition
Fast and accurate scRNA-seq cell type identification
Fast and accurate scRNA-seq cell type identification
fcScan for detecting clusters of coordinates with user defined options
fcScan for detecting clusters of coordinates with user defined options
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Finding the Number of Significant Principal Components
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
Fingerprinting for Flow Cytometry
For Visualizing Differential Expression Analysis
Functional Enrichment analysis
Functional Enrichment analysis
Functional Gene Networks derived from biological enrichment analyses
Functional Network Analysis
Functional Network Analysis
Functional similarities
Functional similarities
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to help analyze data as phyloseq objects
Functions to help analyze data as phyloseq objects
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets
Gene expression-based subtype classification for high-grade serous ovarian cancer
Gene expression-based subtype classification for high-grade serous ovarian cancer
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
gRx Differential Clustering
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
Heterogeneity-Induced Pre-Processing tOol
Heterogeneity-Induced Pre-Processing tOol
Hidden Factor Graph Models
Hierarchical Inference
Hierarchical Inference
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
HLA typing clustering and visualization based on specific similarity metrics
HLA typing clustering and visualization based on specific similarity metrics
Human genome partitioning of dense sequencing data by identifying haplotype blocks
Human genome partitioning of dense sequencing data by identifying haplotype blocks
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 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.
Identify Different Architectures of Sequence Elements
Identify Moonlighting ncRNAs
ILoReg enables high-precision cell population identification from scRNA-Seq data
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Improving replicability in single-cell RNA-Seq cell type discovery
Improving replicability in single-cell RNA-Seq cell type discovery
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Infers biological signatures from gene expression data
Infers clonal composition of a tumor
Integrative clustering of multi-type genomic data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
iSEE Universe
iSEE Universe
iSEE Universe
Iterative Binary Biclustering of Genesets
Iterative Clustering
Iterative Clustering
Iterative Pruning to Capture Population Structure
Iterative Pruning to Capture Population Structure
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
Kernel-Based Analysis Of Biological Sequences
k-Means for k-Nearest Neighbors
LEA: an R package for Landscape and Ecological Association Studies
Linear model and normality based normalization and transformation method (Linnorm)
Linear Models for Microarray Data
Linear Subpsace identification to solve complete gene expression deconvolution problem
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Make Sense to Gene Set Enrichment Analysis Outputs
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
Merging of phenotype information from different cytometric profiles
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH(Medical Subject Headings) Semantic Similarity Measures
Metabarcoding and microbiome analysis using multiple amplicons
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 Single-Cell RNA-Seq Data Analysis
Methods for Single-Cell RNA-Seq Data Analysis
Methods for visualization and statistics on DNA methylation data
Microbial Community Analysis GUI
Microbial Comparative Genomics in R
Microbial Comparative Genomics in R
microRNA-mRNA Integration, Analysis and Network Generation Tool
Mini-batch K-means Clustering for Single-Cell RNA-seq
Mini-batch K-means Clustering for Single-Cell RNA-seq
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
Mirsynergy
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 identify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Model based analysis for paired-end data
Model based analysis for paired-end data
Model-Based Comparative Analysis of the TCR Repertoire
Model-Based Comparative Analysis of the TCR Repertoire
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Monte Carlo Reference-based Consensus Clustering
Monte Carlo Reference-based Consensus Clustering
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Multi Omic Master Regulator Analysis
Multi Omic Master Regulator Analysis
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
Multivariate analysis of microarray data using ADE4
Multivariate Correlation Estimator and Statistical Inference Procedures.
Murine Palate miRNA Expression Analysis
Mutation Order Prediction
Nearest Neighbor Detection for Bioconductor Packages
Nearest Neighbor Detection for Bioconductor Packages
Nearest Neighbor Detection for Bioconductor Packages
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
Network Analysis Supported by Boosting
Network smoothing for scRNAseq
Network smoothing for scRNAseq
Non-parametric Flow Cytometry Data Gating
OnASSIs Ontology Annotation and Semantic SImilarity software
OnASSIs Ontology Annotation and Semantic SImilarity software
PCA Analysis and Visualization for Clustering
Permutation-Based Confidence for Molecular Classification
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phenotyping of microbial Raman spectroscopy data
pipeComp pipeline benchmarking framework
Pipeline for augmented co-expression analysis
Pipelines for Bi-Clustering Using Matrix Factorization
Plot Gene Ontology and KEGG pathway Annotation and Abundance
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility data
Prediction of Protein Conserved Regions Using NADDA Algorithm
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
Projection-based Gating Strategy Optimization for Flow and Mass Cytometry
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)
Protein Profiling
Qualitative biclustering algorithm for expression data analysis in R
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
RBioinf
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reference-Based Single-Cell RNA-Seq Annotation
Reference-Based Single-Cell RNA-Seq Annotation
Reference Index for Cell Types
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
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
RNA-seq analysis using multiple algorithms
RNA-seq analysis using multiple algorithms
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
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 motivated by the SCTC Dream Challenges
runibic: row-based biclustering algorithm for analysis of gene expression data in R
SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data
SAME: Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble for Single-cell RNA-seq Data
Select gold standard including positive and negative genes pairs based on the Gene Ontology
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
Semi-Supervised Mixture Model
Semi-Supervised Mixture Model
Sequential Flow Cytometry Data Gating
Sequential Flow Cytometry Data Gating
Sequential Flow Cytometry Data Gating
SigFuge
SigFuge
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Silly Putty Clustering
Similarity Identification in Gene Expression
Similarity measures for chemical compounds
SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
simple Two-Tier Mapper: an interface for Two-Tier Mapper
Simplify Functional Enrichment Results
Simplify Functional Enrichment Results
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
Single-cell RNA-seq toolkit
Single-cell RNA-seq toolkit
Single Cell Shiny Application for Analysing Single Cell Transcriptomics 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 Transcriptomics Analysis
Spatial Transcriptomics Analysis
SpectralTAD: Hierarchical TAD detection using spectral clustering
SpectralTAD: Hierarchical TAD detection using spectral clustering
SpectralTAD: Hierarchical TAD detection using spectral clustering
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 of the GeneChip
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Subtype Identification with Survival 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
TADCompare: Identification and characterization of differential TADs
TADCompare: Identification and characterization of differential TADs
Targeted, Robust, and Model-free Differential Methylation Analysis
Targeted, Robust, and Model-free 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
Threshing and Reaping for Principal Components
Threshing and Reaping for Principal Components
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
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
TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes
TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes
Tools for analyzing Micro Array experiments
Tools for curating, analyzing, and manipulating biological sequences
Tools for microbiome analysis
Tools for ordering single-cell sequencing
Tools for ordering single-cell sequencing
Tools for Working With Synteny Objects
Tools for Working With Synteny Objects
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.
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
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
Two-Tier Mapper: a clustering tool based on topological data analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
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
Using Cytogenetics Data in R
Using Cytogenetics Data in R
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
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
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
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does TODOELI
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
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis