Bioconductor Packages

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

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

Automatic RNA-Seq present/absent gene expression calls generation

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

Bias-free Footprint Enrichment Test

Processing and analyzing bisulfite sequencing data

Biclustering Analysis and Results Exploration

Binding site defintion based on iCLIP data

Functional Similarities

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

Detect tissue heterogeneity in expression profiles with gene sets

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

Representing Different Biological Sets

Efficient manipulation of biological strings

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

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

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

Cytometry dATa anALYSis Tools

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

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

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

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