A tool for detecting somatic variants in single cell data

WiNGPT是一个基于GPT的医疗垂直领域大模型，旨在将专业的医学知识、医疗信息、数据融会贯通，为医疗行业提供智能化的医疗问答、诊断支持和医学知识等信息服务，提高诊疗效率和医疗服务质量。

R toolkit for single cell genomics

Scaling Single Cell Analysis to Millions of Cells

Analysis of cell-cell communication at single-cell resolution

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene reg…

Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons

MetaTiME: Meta-components in Tumor immune MicroEnvironment

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.

Data-driven Network-based Bayesian Inference of Drivers

Scalable Tool for Gene Network Reverse Engineering

R package for integrating and analyzing multiple single-cell datasets

Dataset distribution for Seurat

NaRnEA (Nonparametric analytical Rank-based Enrichment Analysis)

Run Rstudio Server in a conda environment

R package for Protein activity analysis of single-cell RNAseq.

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

A list of scRNA-seq analysis tools

Bostongene cell deconvolution algorithm from RNAseq

A book covering the fundamentals of data visualization

Tissue specific network for GTEx tissue data (TPM normalized).