Bioconductor Packages

Singular Value Decomposition for Bioconductor Packages

interface to python sklearn via Rstudio reticulate

Transcript expression inference and differential expression analysis for RNA-seq data

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

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

CAncer bioMarker Prediction Pipeline 2 (CAMPP2)

Cytometry dATa anALYSis Tools

Cancer Specific Transcriptomic Signature (CATS)

Perform Chromosomal Ancestry Differences (CAnD) Analyses

CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks

plot bayesian network inferred from gene expression data based on enrichment analysis results

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

Statistical analysis for the Colony Formation Assay

An R package for analysis of case-control studies in genetic epidemiology

Chaos Game Representation for Phylogenetic Analysis

CHARGE: CHromosome Assessment in R from Gene Expression data

Fast and accurate scRNA-seq cell type identification

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

"CITEViz: Classifying Cell Clusters in CITE-Seq Data using the Flow Cytometry Gating Workflow"

Peripheral blood CITE-Seq dataset with 10K cells for use with CITEViz tutorial

Curated Latent-variable Analysis with Molecular Priors

Synthesis of microarray-based classification

Add-on to CellNOptR: Discretized time treatments

ODE add-on to CellNOptR

Bayesian mixture models for copy number polymorphisms

Reliable CNV detection in targeted sequencing applications

Coordinate Covariation Analysis

Multivariate Correlation Estimator and Statistical Inference Procedures.

Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

COexpression Tables ANalysis

CPSM: Cancer patient survival model

Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

CRImage a package to classify cells and calculate tumour cellularity

ChIP-Seq Statistical Power

CTD method for 'connecting the dots' in weighted graphs

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Candidate Driver Analysis

Calibration curves for targeted proteomics, lipidomics and metabolomics data

Cancer subtypes identification, validation and visualization based on multiple genomic data sets

A mass spectrometry imaging toolbox for statistical analysis

This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

Causal network analysis methods

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Reconstruction, visualization and analysis of branching trajectories

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)