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

Analysis Pipeline for Single Cell ATAC-seq

Community-provided extensions to Seurat

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

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

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.

Context specific and dynamic gene regulatory network reconstruction and analysis

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

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

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