Bioconductor Packages

Adaptive Dropout Imputer (ADImpute)

Association Plots

Functional annotation-driven unsupervised clustering for single-cell data

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

Bayesian Analysis of Single-Cell Sequencing data

Stan implementation of BASiCS

Model higher-order methylation profiles

kallisto | bustools R utilities

Batch Effect Correction with Unknow Subtypes for scRNA-seq data

Spatial transcriptomic clustering

Single-cell RNA-seq batch effects correction methods interface

Clustering and Resolution Enhancement of Spatial Transcriptomes

Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Cytometry dATa anALYSis Tools

Plots For Visualising Cell-Cell Interactions

Clustering Deviation Index (CDI)

Fast and accurate scRNA-seq cell type identification

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

COexpression Tables ANalysis

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

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

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Construct Benchmarks for Single Cell Analysis Methods

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

Evaluate Cellspecific Mixing

Reconstruction, visualization and analysis of branching trajectories

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Cepo for the identification of differentially stable genes

Analysis of single-cell epigenomics datasets with a Shiny App

CiteFuse: multi-modal analysis of CITE-seq data

Clustering of Immune Receptor Repertoires

Calculate similarity of clusters from different single cell samples using foldchanges

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

Power analysis for CyTOF experiments

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Differential Composition Analysis Transformed by a Similarity matrix

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

Genome-wide Detection of Differential ORF Usage

Convenient functions to streamline your single cell data analysis workflow

Helper Functions for LIBD Deconvolution

DenoIST: Denoising Image-based Spatial Transcriptomics data

Differentially regulated genes from scRNA-seq 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

Expression Weighted Celltype Enrichment

Annotate cell types for scRNA-seq data

FEAture SelcTion (FEAST) for Single-cell clustering