Biocview "Classification"

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 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

Analysis of Large-Scale Pharmacogenomic Data

Analysis of Large-Scale Radio-Genomic Data

Analysis of patient-derived xenograft (PDX) data

Analysis of single-cell epigenomics datasets with a Shiny App

An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

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

An R package for the Bayesian analysis of differential subcellular localisation experiments

Application of gene classifiers

Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations

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 Predicting Cell Cycle Progression Using Single-Cell RNA-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 unsupervised projection of single cell RNA-seq data

A toolkit for single-cell immune receptor profiling

A unifying bioinformatics framework for spatial proteomics

Automated Affymetrix Array Analysis Classification Package

Automated Affymetrix Array Analysis Core Package

Automated spectraL Processing System for NMR

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

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

Build MultiClass Pair-Based Classifiers using TSPs or RF

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 type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

Cepo for the identification of differentially stable genes

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

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 Sequences using Complex Network and Information Theory

Classification using generalized partial least squares

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

Cluster and Tree Conversion.

Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Comparison and Visualization of Ranking and Assignment Methods

Comprehensive Annotation of Predictive Features for Interval-based Genomic Data

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

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

Detection, Characterization and Visualization of Kataegis in Sequencing Data

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

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Dual KS Discriminant Analysis and Classification

Dual redundant reference sequencing

Easy single cell analysis platform for enrichment

Ensemble of Gene Set Enrichment Analyses

Epigenetic and gene transcription data normalization and integration with mixture models

Estimate Systems Immune Response from RNA-seq data

Evaluation of Bioinformatics Metrics

Exposome exploration and outcome data analysis

Expression data analysis via the Iterative Signature Algorithm

Fast and accurate scRNA-seq cell type identification

Fast Correlation Based Filter for Feature Selection

FASTQ2OTU: Automate microbiome analyses

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

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

Gene expression-based subtype classification for high-grade serous ovarian cancer

Gene Expression Variation Analysis (GEVA)

Genomic Visualizations in R

genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)

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

Hidden Variable Dynamic Modeling

Hierarchical ensemble method based on factor graph

Identification and classification of plant transcription factors

Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning

Identification of enriched motif pairs from chromatin interaction data

Identification of SNP Interactions

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

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Interface to the RDP Classifier

Irreproducible Discovery Rate for Genomic Interactions Data

Iterative Differential Clustering for single-cell

Kernel-Based Analysis Of Biological Sequences

k-Means for k-Nearest Neighbors

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Learning from DNA to Predict Enhancers

LinkHD: a versatile framework to explore and integrate heterogeneous data

Machine Learning Interface for RNA-Seq Data

Marker Enrichment Modeling (MEM)

massiR: MicroArray Sample Sex Identifier

Mechanism-Aware Imputation

Metabarcoding and microbiome analysis using multiple amplicons

Methods for Continuous Flow Cytometry

Methods for TCR single-cell embedding

Methods for visualization and statistics on DNA methylation data

MicroArray Gene-expression-based Program In Error rate estimation

Microbiome Exploration App

Minimized Single-Cell Consensus Clustering

miRNAtap: microRNA Targets - Aggregated Predictions

Miscellaneous Functions for Metabarcoding Analysis

Misclassification error estimation with cross-validation

Misclassification Penalized Posterior Classification

'(m,n)-mer' - A Simple Statistical Feature for Sequence Classification

Model based analysis for paired-end data

MoPS - Model-based Periodicity Screening

Multilevel Model for Multivariate Responses with Missing Values

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Multiple co-inertia analysis of omics datasets

Multivariate analysis of microarray data using ADE4

Nearest Neighbor Detection for Bioconductor Packages

NetPathMiner for Biological Network Construction, Path Mining and Visualization

Network-based patient classifier

Network Centrality Metrics for Elastic-Net Regularized Models

NEUral network-based single-Cell Annotation tool

Normalization and difference calling in ChIP-seq data

Objective Assessment of Copy-Number Estimates

Omics Data Integration Project

Ontology traversal and search

Open Cancer TherApeutic Discovery (OCTAD)

PAA (Protein Array Analyzer)

Package for enabling powerful shiny web displays of Bioconductor objects

Pancreatic Ductal Adenocarcinoma Tool-Kit

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

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.

PLSDA-batch

preciseTAD: A machine learning framework for precise TAD boundary prediction

Prediction of Oligomerization of Coiled Coil Proteins

Predict open reading frames in nucleotide sequences

Pretrained learning models for cell type prediction on single cell RNA-sequencing data

PRObabilistic Pathway Score (PROPS)

Quantification of the Tumor Immune contexture from RNA-seq data

Random Gene Set Enrichment Analysis

RBioinf

Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers

Reference-Based Single-Cell RNA-Seq Annotation

Refine muscle-invasive bladder cancer

Reliable CNV detection in targeted sequencing applications

Replication stress-related prognostic index in HCC

R implementation of the LEfSE method for microbiome biomarker discovery

RLSeq: An analysis package for R-loop mapping data

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

scClassify: single-cell Hierarchical Classification

SCFA: Subtyping via Consensus Factor Analysis

scReClassify: post hoc cell type classification of single-cell RNA-seq data

ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

Semi-Supervised Mixture Model

sigFeature: Significant feature selection using SVM-RFE & t-statistic

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

Single-Cell Consensus Clustering

Single-Cell Operation for Neat Enrichment

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

ssPATHS: Single Sample PATHway Score

Statistical analysis for sparse high-throughput sequencing

Statistical Analysis of MPRA data

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

Summarize, Analyze and Visualize MAF Files

Supervised mutational signatures

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 Iterative Bayesian Model Averaging (BMA) algorithm

The scigenex package (Single-Cell Informative GENe Explorer)

Time-Course Multi-Omics data integration

TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes

Tools for Assessing Clustering

Tools for Omics Data Analysis

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 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

Transcriptional Rewiring

Two-Tier Mapper: a clustering tool based on topological data analysis

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

Variational Bayesian Multinomial Probit Regression

Visualize biclusters identified in gene expression data

What the Package Does (One Line, Title Case)

What the Package Does TODOELI

Biocview "Classification"

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