Single-Cell Omics Integration ML Frameworks

Tools for integrating, embedding, and analyzing single-cell and spatial omics data through deep learning and dimensionality reduction. Does NOT include bulk omics analysis, general multi-omics survey papers, or microbiome annotation workflows.

There are 84 single-cell omics integration frameworks tracked. 4 score above 70 (verified tier). The highest-rated is scverse/scanpy at 95/100 with 2,367 stars and 740,313 monthly downloads. 2 of the top 10 are actively maintained.

Get all 84 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	scverse/scanpy Single-cell analysis in Python. Scales to >100M cells.	95	Verified	2,367	Python
2	scverse/scvi-tools Deep probabilistic analysis of single-cell and spatial omics data	95	Verified	1,582	Python
3	Teichlab/celltypist A tool for semi-automatic cell type classification	76	Verified	458	Python
4	theislab/scarches Reference mapping for single-cell genomics	70	Verified	400	Jupyter Notebook
5	Teichlab/cellhint A tool for semi-automatic cell type harmonization and integration	68	Established	118	Python
6	Lotfollahi-lab/nichecompass End-to-end analysis of spatial multi-omics data	60	Established	104	Python
7	earmingol/cell2cell User-friendly tool to infer cell-cell interactions and communication from...	57	Established	79	Python
8	scverse/cellrank CellRank: dynamics from multi-view single-cell data	57	Established	433	Python
9	JCVenterInstitute/NSForest A machine learning method for the discovery of the minimum marker gene...	57	Established	68	HTML
10	sldyns/SpaHDmap Deep fusion of spatial transcriptomics and histology images for...	56	Established	17	Python
11	ratschlab/DeepSpot DeepSpot: Deep learning model for predicting spatial transcriptomics from...	56	Established	65	Jupyter Notebook
12	scDataset/scDataset scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics	54	Established	43	Jupyter Notebook
13	jsxlei/SCALEX Online single-cell data integration through projecting heterogeneous...	54	Established	83	Jupyter Notebook
14	eleozzr/desc Deep Embedding for Single-cell Clustering	53	Established	89	Jupyter Notebook
15	OmicsML/dance DANCE: a deep learning library and benchmark platform for single-cell analysis	52	Established	384	Python
16	yi-zhang/STHD STHD: probabilistic cell typing of Single spots in whole Transcriptome...	51	Established	37	Jupyter Notebook
17	vanvalenlab/deepcell-tf Deep Learning Library for Single Cell Analysis	50	Established	474	Python
18	labomics/midas PyTorch implementation of the MIDAS algorithm for single-cell multimodal...	50	Established	62	Python
19	saeyslab/harpy Single-cell spatial omics analysis that makes you happy!	49	Emerging	52	Python
20	ma-compbio/Higashi single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph	48	Emerging	92	Jupyter Notebook
21	himelmallick/IntegratedLearner Integrated Machine Learning for Multi-omics Classification and Prediction	46	Emerging	27	HTML
22	ttgump/scDeepCluster scDeepCluster for Single Cell RNA-seq data	46	Emerging	105	Jupyter Notebook
23	ZJUFanLab/bulk2space a spatial deconvolution method based on deep learning frameworks, which...	45	Emerging	134	Jupyter Notebook
24	SCCAF/sccaf Single-Cell Clustering Assessment Framework	45	Emerging	108	Jupyter Notebook
25	xinglab-ai/genomap Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell...	44	Emerging	19	Python
26	LiQian-XC/sctour A deep learning architecture for robust inference and accurate prediction of...	44	Emerging	79	Python
27	tanjimin/C.Origami C.Origami, a prediction and screening framework for cell type-specific 3D...	43	Emerging	84	Python
28	zhangxiaoyu11/OmiEmbed Multi-task deep learning framework for multi-omics data analysis	43	Emerging	50	Python
29	yizhak-lab-ccg/scXpand scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing	43	Emerging	8	Python
30	MICS-Lab/scyan Biology-driven deep generative model for cell-type annotation in cytometry....	43	Emerging	42	Python
31	EinarOlafsson/spacr spaCR Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR)	41	Emerging	6	Python
32	andreariba/DeepCycle Cell cycle inference in single-cell RNA-seq	39	Emerging	50	Python
33	ratschlab/DeepSpot2Cell DeepSpot2Cell: Predicting virtual single-cell spatial transcriptomics from...	39	Emerging	8	Jupyter Notebook
34	poseidonchan/TAPE Deep learning-based tissue compositions and cell-type-specific gene...	39	Emerging	59	Jupyter Notebook
35	ttgump/scDeepCluster_pytorch Pytorch implementation of scDeepCluster for Single Cell RNA-seq data	39	Emerging	34	Jupyter Notebook
36	AI4SCR/MatchCLOT Python package implementing our method MatchCLOT for multimodal single-cell...	39	Emerging	14	Jupyter Notebook
37	jan-forest/autoencodix_package Python library for multi-omics data integration by autoencoders	39	Emerging	8	Jupyter Notebook
38	DLS5-Omics/CellNavi CellNavi is a deep learning framework designed to predict genes driving...	38	Emerging	46	Python
39	Ashford-A/UniVI UniVI is a scalable multi-modal VAE toolkit for aligning heterogeneous...	38	Emerging	5	Jupyter Notebook
40	devCellPy-Team/devCellPy devCellPy is a Python package designed for hierarchical multilayered...	38	Emerging	28	Jupyter Notebook
41	ma-compbio/SpiceMix spatial transcriptome, single cell	37	Emerging	74	Jupyter Notebook
42	gao-lab/SLAT Spatial-Linked Alignment Tool	37	Emerging	90	Python
43	quhaichao/SpaCon SpaCon, a deep-learning method that integrates spatial transcriptomic data...	37	Emerging	2	Jupyter Notebook
44	scapeML/scape Single-cell Analysis of Perturbational Effects using Machine Learning	36	Emerging	17	Python
45	Jwindler/AutoHiC A novel genome assembly pipeline based on deep learning	34	Emerging	69	Python
46	Trhova/Multi-omics Intuitive guide to multi-omics integration with toy examples: supervised...	34	Emerging	76	Python
47	theislab/cellrank_reproducibility CellRank's reproducibility repository.	32	Emerging	16	Jupyter Notebook
48	ma-compbio/Fast-Higashi single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition	31	Emerging	20	Jupyter Notebook
49	praneet1988/ELeFHAnt Ensemble Learning for Harmonization and Annotation of Single Cells...	31	Emerging	23	R
50	enveda/sparc-multiomics SPARC CCF Multi-omics analysis	31	Emerging	3	Jupyter Notebook
51	Noble-Lab/HiCFoundation HiCFoundation is a generalizable Hi-C foundation model for chromatin...	31	Emerging	25	Python
52	ZoyavanMeel/ORCA Origin of Chromosomal Replication Assessment. Python tool for the analysis...	30	Emerging	18	Python
53	jiazhao97/INSPIRE INSPIRE: interpretable, flexible and spatially-aware integration of multiple...	30	Emerging	8	Python
54	WPZgithub/CEFCON Deciphering driver regulators of cell fate decisions from single-cell RNA-seq data	30	Emerging	29	Jupyter Notebook
55	YangLabHKUST/MacSGP MacSGP: Mapping Cell-Type-Specific Spatial Gene Programs Uncovers Tissue...	29	Experimental	3	Python
56	phipsonlab/cellXY R package to predict sex of single cells and identify Male/Female doublets...	29	Experimental	8	R
57	Noble-Lab/CellCycleNet Predicting cell cycle stage from 3D single-cell nuclear-stained images	28	Experimental	10	Python
58	bnediction/scBoolSeq scBoolSeq: scRNA-Seq data binarisation and synthetic generation from Boolean dynamics	27	Experimental	13	Python
59	j-rub/scVital Deep Learning Algorithm for cross-species integration of scRNA-seq data	27	Experimental	3	Jupyter Notebook
60	ttgump/scDHMap Model-based deep hyperbolic manifold learning for visualizing complex...	26	Experimental	8	Jupyter Notebook
61	hip-satomi/ObiWan-Microbi Omero based integrated Workflow for annotating Microbes in the Cloud	26	Experimental	6	Dockerfile
62	Novartis/scar scAR (single-cell Ambient Remover) is a deep learning model for removal of...	25	Experimental	58	Python
63	ma-compbio/scGHOST single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome...	23	Experimental	21	Jupyter Notebook
64	saeyslab/ViVAE Single-cell dimensionality reduction toolkit	23	Experimental	11	Jupyter Notebook
65	ratschlab/he2st Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced...	22	Experimental	13	Jupyter Notebook
66	HelloWorldLTY/AWGAN Codes for paper: AWGAN: A Powerful Batch Effect Removal Model for scRNA-seq Data	22	Experimental	8	Jupyter Notebook
67	infocusp/scaLR Single cell analysis using Low Resource	21	Experimental	20	Python
68	gao-lab/PASSAGE Phenotype Associated Spatial Signature Analysis with Graph-based Embedding	20	Experimental	26	Jupyter Notebook
69	ngalioto/arch3d ARCH3D: A foundation model for global genome architecture	20	Experimental	1	Python
70	sifrimlab/MIMA Multimodal Integration with Modality-agnostic Autoencoders - Developed by...	20	Experimental	9	Jupyter Notebook
71	aapupu/MIST An interpretable and flexible deep learning framework for single-T cell...	20	Experimental	14	Jupyter Notebook
72	sionaris/MultiOmicsSurvey A comprehensive survey on computational methods used for multi-omic analysis...	19	Experimental	—	R
73	TomMakesThings/Clustering-and-TDA-of-scRNA-seq-Data Final year project experimenting with clustering and topological data...	19	Experimental	9	Jupyter Notebook
74	diegommcc/SpatialDDLS Deconvolution of spatial transcriptomics data based on Deep Learning	18	Experimental	6	R
75	C0nc/TAICHI A Python package for the Scalable and accurate identification...	18	Experimental	11	Jupyter Notebook
76	rockdeme/chrysalis Powerful and lightweight package to identify tissue compartments in spatial...	17	Experimental	18	Jupyter Notebook
77	evan950608/NYCU_BMI_scRNA_study Source code for the study "Marker Gene Identification Algorithm of Precision...	14	Experimental	—	Jupyter Notebook
78	Lorenzodruif/cells 🧬 Simplify data manipulation with Cells, a lightweight framework for...	14	Experimental	—	HTML
79	mathisbouvet/Advanced-Spatial-Omics-Pipeline Python-based pipeline for segmentation quality control and unsupervised...	14	Experimental	—	—
80	Brothers15691/Multi-omics 🔍 Explore multi-omics integration with DIABLO, DIVAS, and VAEs, providing...	14	Experimental	—	Python
81	dianalaplace/ivd-ecm-regeneration-ml ML-driven identification of ECM-regenerative gene signatures in human...	14	Experimental	—	—
82	johramoosa/single-cell-ml-analysis End-to-end single-cell RNA-seq ML pipeline: clustering, annotation, and...	14	Experimental	—	Jupyter Notebook
83	GiatrasKon/scRNAseq-Analysis-Pipeline Comprehensive OOP Python-implemented pipeline for analyzing single-cell...	13	Experimental	5	Jupyter Notebook
84	djimenezsanchez/CellEmbeddings A fully unsupervised learning method that encodes cell phenotypes,...	12	Experimental	4	C++

Comparisons in this category

scanpy and scvi-tools (95 vs 95) scanpy and scXpand (95 vs 43)