Bioconductor Packages

Basic peak calling on STARR-seq data

Batch Effects Quality Control Software

Identify Batch-Biased Spatially Variable Genes

Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data

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

Processing and analyzing bisulfite sequencing data

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

Efficient manipulation of biological strings

Code for using BridgeDb identifier mapping framework from within R

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

Collection of annotation related methods for mass spectrometry data

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

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

Plots For Visualising Cell-Cell Interactions

Co-expression Modules identification Tool

Statistical analysis for the Colony Formation Assay

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

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

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

Combinatorial Polyfunctionality Analysis of Single Cells

Cell OrderiNg by FluorEScence Signal

Data normalization by matrix raking

COexpression Tables ANalysis

Design of guide RNAs in CRISPR genome-editing systems

CRImage a package to classify cells and calculate tumour cellularity