single-cell-analysis
There are 180 repositories under single-cell-analysis topic.
sqjin/CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
immunomind/immunarch
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
r3fang/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
satijalab/seurat-wrappers
Community-provided extensions to Seurat
DingWB/PyComplexHeatmap
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
jinworks/CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
slowkow/harmonypy
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
sunduanchen/Scissor
Scissor package
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
quadbio/scRNAseq_analysis_vignette
Tutorial for scRNA-seq data analysis beginners using R
dynverse/dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
pinellolab/dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
GregorySchwartz/too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
yanwu2014/swne
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
JEFworks-Lab/HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
singleron-RD/CeleScope
Single Cell Analysis Pipelines
powellgenomicslab/Nebulosa
R package to visualize gene expression data based on weighted kernel density estimation
sankaranlab/SCAVENGE
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
labsyspharm/scimap
Spatial Single-Cell Analysis Toolkit
chriscainx/mnnpy
An implementation of MNN (Mutual Nearest Neighbors) correct in python.
gao-lab/SLAT
Spatial-Linked Alignment Tool
dynverse/dyngen
Simulating single-cell data using gene regulatory networks 📠
poseidonchan/TAPE
Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)
quadbio/scMultiome_analysis_vignette
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
zjunlp/ChatCell
ChatCell: Facilitating Single-Cell Analysis with Natural Language
berenslab/umi-normalization
Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology
wanglab-broad/ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
theislab/pseudodynamics
Dynamic models for single-cell RNA-seq time series.
genecell/COSG
Accurate and fast cell marker gene identification with COSG
RabadanLab/randomly
A Library for Denoising Single-Cell Data with Random Matrix Theory
ciccalab/SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
KChen-lab/bindSC
Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data
nasqar/seuratv3wizard
A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
SGI-LungCancer/SingleCell
Code repository for single cell RNA-seq
YangLabHKUST/Portal
Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets