Bioconductor Packages

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

Clustering and Resolution Enhancement of Spatial Transcriptomes

Compression of Illumina BeadArray data

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

Bioinformatics Genetic Algorithm (BioGA)

Routines for the functional analysis of biological networks

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

View AnnotationHub and ExperimentHub Resources Interactively

View Bioconductor Package Maintainer Information Interactively

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

Collection of annotation related methods for mass spectrometry data

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Cytometry dATa anALYSis Tools

Case Control Allele Frequency Estimation

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

Plots For Visualising Cell-Cell Interactions

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

CGHbase: Base functions and classes for arrayCGH data analysis.

Normalization of array CGH data with imbalanced aberrations.

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

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

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

Combinatorial Polyfunctionality Analysis of Single Cells

Data normalization by matrix raking

COexpression Tables ANalysis

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

Design of guide RNAs in CRISPR genome-editing systems

Statistical tools for the analysis of ChIP-seq data

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