Bioconductor Packages

Spatial transcriptomic clustering

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Basic peak calling on STARR-seq data

Batch Effects Quality Control Software

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Clustering and Resolution Enhancement of Spatial Transcriptomes

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Bias-free Footprint Enrichment Test

Biclustering Analysis and Results Exploration

Binding site defintion based on iCLIP data

Functional Similarities

Model-View-Controller (MVC) Classes That Use Biobase

Biological Network Analysis in R

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

Detect tissue heterogeneity in expression profiles with gene sets

Nearest Neighbor Detection for Bioconductor Packages

Singular Value Decomposition for Bioconductor Packages

interface to python sklearn via Rstudio reticulate

Efficient manipulation of biological strings

Cohort-aware methods for intrinsic molecular subtyping of breast cancer

Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics

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

Cytometry dATa anALYSis Tools

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

Case Control Allele Frequency Estimation

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

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

Synthesis of microarray-based classification

A normalization method for Copy Number Aberration in cancer samples

CNE Detection and Visualization

Add-on to CellNOptR: Discretized time treatments

Integration of CellNOptR to add missing links

ODE add-on to CellNOptR

Copy Number Variant Metrics

Reliable CNV detection in targeted sequencing applications

Summarization and expression/phenotype association of CNV ranges

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

Coordinate Covariation Analysis

Data normalization by matrix raking

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