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 86 single-cell omics integration frameworks tracked. 2 score above 70 (verified tier). The highest-rated is scverse/scanpy at 82/100 with 2,367 stars. 2 of the top 10 are actively maintained.

Get all 86 projects as JSON

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

Comparisons in this category

scvi-tools and scanpy (82 vs 82) scanpy and scXpand (82 vs 49)