Biocview "Classification"

Accurate, high-resolution sample inference from amplicon sequencing data
Accurate, high-resolution sample inference from amplicon sequencing data
A collection of tools for imaging MS data processing
Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
A Framework for Consensus Partitioning
A Framework for Consensus Partitioning
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
A lecture on sequence count data
A mass spectrometry imaging toolbox for statistical analysis
AmiGO visualize R interface
A Minimum Enclosing Ball (MEB) method to detect differential expression genes for RNA-seq data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of patient-derived xenograft (PDX) data
Analysis of patient-derived xenograft (PDX) data
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
An R package for nucleosome positioning prediction
Application of gene classifiers
Application of gene classifiers
Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations
Assign Properties to TNBC Patients
Assign Properties to TNBC Patients
Assign rfPred functional prediction scores to a missense variants list
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning
A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
Base package for enabling powerful shiny web displays of Bioconductor objects
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
BGAfun A method to identify specifity determining residues in protein families
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
cell counter
Cell OrderiNg by FluorEScence Signal
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Classification and Feature Selection for 'Omics' Datasets
Classification and Feature Selection for 'Omics' Datasets
Classification by local similarity threshold
Classification for Biological Sequences
Classification of Microarray Samples using Penalized Discriminant Methods
Classification of RNA-seq data from ALL samples
Classification of RNA-seq data from ALL samples
Classification using generalized partial least squares
Classification using generalized partial least squares
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
Classify diseases and build associated gene networks using gene expression profiles
Classify Samples From RNA-Seq Datasets
Clonality testing
Clonality testing
Cluster and Tree Conversion.
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
Collection of Cell Type Reference Datasets
Comparison and Visualization of Ranking and Assignment Methods
Comparison and Visualization of Ranking and Assignment Methods
Comparison and Visualization of Ranking and Assignment Methods
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational comparisons of cytometry profiles
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Computation of Gene Expression-Based Signatures in Breast Cancer
Computation of Gene Expression-Based Signatures in Breast Cancer
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
CRImage a package to classify cells and calculate tumour cellularity
Data Mining for RNA-seq data: normalization, feature selection and classification
Data Mining for RNA-seq data: normalization, feature selection and classification
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
Development and validation of diagnostic tests from high-dimensional molecular data
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Different distance measures
Different distance measures
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Dual KS Discriminant Analysis and Classification
Dual redundant reference sequencing
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Epigenetic and gene transcription data normalization and integration with mixture models
Evaluation of Bioinformatics Metrics
Evaluation of Bioinformatics Metrics
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Expression data analysis via the Iterative Signature Algorithm
Fast and accurate scRNA-seq cell type identification
Fast and accurate scRNA-seq cell type identification
Fast Correlation Based Filter for Feature Selection
Fast Correlation Based Filter for Feature Selection
fastseg - a fast segmentation algorithm
flexible pipelines for secretome prediction
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
GaGa hierarchical model for high-throughput data analysis
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
Genomic Visualizations in R
Genomic Visualizations in R
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
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
Hidden Variable Dynamic Modeling
Identification of SNP Interactions
Identification of SNP Interactions
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Implementation of gene expression anti-profiles
Inferring unobserved perturbations from gene expression data
Infers biological signatures from gene expression data
Information Accretion-based Function Predictor Evaluation
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Interface to the Basic Local Alignment Search Tool (BLAST)
Interface to the RDP Classifier
Irreproducible Discovery Rate for Genomic Interactions Data
Irreproducible Discovery Rate for Genomic Interactions Data
Kernel-Based Analysis Of Biological Sequences
k-Means for k-Nearest Neighbors
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
Learning from DNA to Predict Enhancers
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Marker Enrichment Modeling (MEM)
Marker Enrichment Modeling (MEM)
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
Metabarcoding and microbiome analysis using multiple amplicons
Methods for Continuous Flow Cytometry
Methods for visualization and statistics on DNA methylation data
MicroArray Gene-expression-based Program In Error rate estimation
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
miRNAtap: microRNA Targets - Aggregated Predictions
Misclassification error estimation with cross-validation
Misclassification Penalized Posterior Classification
Model based analysis for paired-end data
Model based analysis for paired-end data
MoPS - Model-based Periodicity Screening
Multilevel Model for Multivariate Responses with Missing Values
Multiple co-inertia analysis of omics datasets
Multiple co-inertia analysis of omics datasets
Multivariate analysis of microarray data using ADE4
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-based patient classifier
Network-based patient classifier
Network Centrality Metrics for Elastic-Net Regularized Models
Network Centrality Metrics for Elastic-Net Regularized Models
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Objective Assessment of Copy-Number Estimates
Omics Data Integration Project
Omics Data Integration Project
Omics Data Integration Project
Ontology traversal and search
PAA (Protein Array Analyzer)
Package for enabling powerful shiny web displays of Bioconductor objects
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
Permutation-Based Confidence for Molecular Classification
Permutation filtration for microbiome data
Permutation filtration for microbiome data
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
pIR: Estimating Isoelectric Point (pI) of Peptide and Proteins from Amino Acid Sequence.
Prediction of Oligomerization of Coiled Coil Proteins
Prediction of Oligomerization of Coiled Coil Proteins
PRObabilistic Pathway Score (PROPS)
PRObabilistic Pathway Score (PROPS)
Random Gene Set Enrichment Analysis
RBioinf
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
Reference-Based Single-Cell RNA-Seq Annotation
Reference-Based Single-Cell RNA-Seq Annotation
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Robust prediction of clinical outcomes using cytometry data without cell gating
Robust prediction of clinical outcomes using cytometry data without cell gating
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
Sample Classifier
Sample Classifier
scClassify: single-cell Hierarchical Classification
scClassify: single-cell Hierarchical Classification
Semi-Supervised Mixture Model
Semi-Supervised Mixture Model
sigFeature: Significant feature selection using SVM-RFE & t-statistic
sigFeature: Significant feature selection using SVM-RFE & t-statistic
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Signature discovery from omics data
Similarity Identification in Gene Expression
simple Two-Tier Mapper: an interface for Two-Tier Mapper
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical Analysis of MPRA data
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
Stepwise Classification of Cancer Samples using High-dimensional Data Sets
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
Synthesis of microarray-based classification
Synthesis of microarray-based classification
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 Iterative Bayesian Model Averaging (BMA) algorithm
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes
TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes
Tools for performing taxonomic assignment.
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells.
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.
Transcriptional Data Guided fMRI Network Classification
Two-Tier Mapper: a clustering tool based on topological data analysis
Two-Tier Mapper: a clustering tool based on topological data analysis
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Variational Bayesian Multinomial Probit Regression
Visualize biclusters identified in gene expression data
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does TODOELI