Bioconductor Packages

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

Automated spectraL Processing System for NMR

Computational pipeline for computing probability of modification from structure probing experiment data

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Nearest Neighbor Detection for Bioconductor Packages

Cohort-aware methods for intrinsic molecular subtyping of breast cancer

Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

Fast and accurate scRNA-seq cell type identification

Synthesis of microarray-based classification

Reliable CNV detection in targeted sequencing applications

CRImage a package to classify cells and calculate tumour cellularity

A mass spectrometry imaging toolbox for statistical analysis

Cepo for the identification of differentially stable genes

Analysis of single-cell epigenomics datasets with a Shiny App

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Clustering of Immune Receptor Repertoires

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

An R package for colorectal cancer screening and microbiome analysis

Robust prediction of clinical outcomes using cytometry data without cell gating

Data Mining for RNA-seq data: normalization, feature selection and classification

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

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Ensemble of Gene Set Enrichment Analyses

GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

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

Genomic Visualizations in R

Classification of Helicobacter Pylori Genomes

HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C

Comparative analysis of RNA-seq data for hybrids and their progenitors

Methods for BCR single-cell embedding

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Learning from DNA to Predict Enhancers

Mechanism-Aware Imputation

A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data

Uniform interfaces to R machine learning procedures for data in Bioconductor containers

Machine Learning Interface for RNA-Seq Data

Statistical Analysis of MPRA data

A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

Misclassification Penalized Posterior Classification

NetPathMiner for Biological Network Construction, Path Mining and Visualization

Predict open reading frames in nucleotide sequences

PAA (Protein Array Analyzer)

Pancreatic Ductal Adenocarcinoma Tool-Kit

Phenotypes Identification Using Mapper from topological data Analysis

PLSDA-batch

Tools for Omics Data Analysis