Bioconductor Packages

Adaptive Dropout Imputer (ADImpute)

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Accessing AlphaMissense Data Resources in R

Bayesian Analysis of Single-Cell Sequencing data

Stan implementation of BASiCS

Computational pipeline for computing probability of modification from structure probing experiment data

Identify Batch-Biased Spatially Variable Genes

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

Clustering and Resolution Enhancement of Spatial Transcriptomes

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

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

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

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

Co-expression Modules identification Tool

Data normalization by matrix raking

COexpression Tables ANalysis

Data companion to CTexploreR

Explores Cancer Testis Genes

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

Causal network analysis methods

Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis

Evaluate Cellspecific Mixing

Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

Queries the Human Cell Atlas

Identifies differentially expressed genes with respect to other local genes

DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Helper Functions for LIBD Deconvolution

DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results

DenoIST: Denoising Image-based Spatial Transcriptomics data

Normalization of Single-Cell mRNA Sequencing Data

Utilities for Handling Single-Cell Droplet Data

Improving replicability in single-cell RNA-Seq cell type discovery

Analysis of the data from RNA duplex probing experiments

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

GEOexplorer: a webserver for gene expression analysis and visualisation

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

Pipeline for augmented co-expression analysis

Tools for spliced gene structure manipulation and analysis

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Delineate outstanding genomic zones of differential gene activity

Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

NanoString GeoMx Tools

S4 Class for Quantitative Data and Associated Networks

Hierarchical Variance Partitioning

Comparative analysis of RNA-seq data for hybrids and their progenitors

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Individual-Specific ceLl typE referencing Tool

InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics