Bioconductor Packages

Routines for the functional analysis of biological networks

R-side access to BioPlex protein-protein interaction data

BioTIP: An R package for characterization of Biological Tipping-Point

Representing Different Biological Sets

"Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al. - experimental data and complete analysis

This R package for performing module repertoire analyses and generating fingerprint representations

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

Chromosmal Aberrations Finder in Expression data

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

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

Case Control Allele Frequency Estimation

PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

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

CGHbase: Base functions and classes for arrayCGH data analysis.

Dimension Reduction for Array CGH Data with Minimal Information Loss.

Fast and accurate scRNA-seq cell type identification

A normalization method for Copy Number Aberration in cancer samples

Add-on to CellNOptR: Discretized time treatments

Integration of CellNOptR to add missing links

ODE add-on to CellNOptR

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

Copy Number Variant Metrics

Reliable CNV detection in targeted sequencing applications

Summarization and expression/phenotype association of CNV ranges

Identifies false positives of CNV calling tools by using SNV calls

Copy Number Visualization

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Coordinate Covariation Analysis

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Annotations for City of Hope CpG Island Analysis Pipeline

COexpression Tables ANalysis

CPSM: Cancer patient survival model

Statistical tools for the analysis of ChIP-seq data

Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps

Genomic coordinates of CTCF binding sites, with orientation

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

Data companion to CTexploreR

Explores Cancer Testis Genes

Candidate Driver Analysis

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

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

Predict genes expressed selectively in specific cell types

Evaluate Cellspecific Mixing

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