R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Community-provided extensions to Seurat

Analysis Pipeline for Single Cell ATAC-seq

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

Scissor package

Haplotype-aware CNV analysis from single-cell RNA-seq

Tutorial for scRNA-seq data analysis beginners using R

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

A collection of 50+ trajectory inference methods within a common interface 📥📤

Context specific and dynamic gene regulatory network reconstruction and analysis

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

Cluster single cells and analyze cell clade relationships with colorful visualizations.

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

Single Cell Analysis Pipelines

R package to visualize gene expression data based on weighted kernel density estimation

Spatial-Linked Alignment Tool