Graph-linked unified embedding for single-cell multi-omics data integration
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Nov 10, 2025 - Python
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single-cell-multiomics
Here are 23 public repositories matching this topic...
Context specific and dynamic gene regulatory network reconstruction and analysis
network-inference network-visualization network-analysis single-cell-analysis gene-regulatory-network dynamic-network single-cell-multiomics single-cell-network
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Nov 24, 2025 - Python
R package to visualize gene expression data based on weighted kernel density estimation
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Feb 27, 2024 - R
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
bioinformatics tutorial single-cell-rna-seq single-cell-analysis single-cell-atac-seq single-cell-multiomics
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Apr 22, 2024
PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
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Dec 3, 2025 - Python
Accurate and fast cell marker gene identification with COSG
single-cell marker-genes single-cell-rna-seq single-cell-analysis single-cell-atac-seq spatial-transcriptomics single-cell-multiomics
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Oct 17, 2025 - Python
𝒫robabilistic modeling of RNA velocity ⬱
probabilistic-programming transcriptomics pyro probabilistic-models single-cell-genomics single-cell-rna-seq rna-velocity-estimation multiomics deep-generative-model developmental-trajectories rna-velocity rna-splicing single-cell-multiomics cell-fate-determination rna-splicing-analysis
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Dec 19, 2025 - Python
An unsupervised approach for the integrative analysis of single-cell multi-omics data
integrative-analysis single-cell-multiomics single-cell-multimodal-omics simultaneous-measurements sparse-epigenomic-profile
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Nov 16, 2020 - R
Python package implementing our method MatchCLOT for multimodal single-cell data integration
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May 19, 2023 - Jupyter Notebook
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
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Jul 29, 2023 - R
R and MATLAB scripts for MAGICAL
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Jun 26, 2024 - R
Luo Lab snmCT-seq bioinformatics pipeline for joint single-nucleus methylation & transcriptome profiles.
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Mar 17, 2024 - Jupyter Notebook
scMagnify is a versatile Python toolkit for inferring and analyzing gene regulatory networks (GRNs) from single-cell multi-omic datasets
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Dec 3, 2025 - Python
SCOIT is an implementation of a probabilistic tensor decomposition framework for single-cell multi-omics data integration.
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Dec 12, 2024 - Python
bioinformatics pipeline for single-nucleus methylation & chromatin conformation capture assay (sn-m3C-seq)
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May 20, 2024 - Jupyter Notebook
Single-cell eQTL mapping and causal gene regulatory network inference at high efficiency and accuracy
causal-inference gene-regulatory-network mendelian-randomization scrna-seq-analysis eqtl-mapping single-cell-multiomics
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Dec 19, 2025 - Python
Code and guides for the SCRGOT Coder Upgrade single cell analysis workshop
education bioinformatics single-cell-rna-seq single-cell-analysis spatial-transcriptomics single-cell-multiomics
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May 14, 2025 - R
Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease
kidney single-cell copy-number-variation single-cell-genomics single-cell-rna-seq single-cell-atac-seq aneuploidy spatial-transcriptomics ckd single-cell-multiomics loss-of-y-chromosome mosaic-chromosomal-alterations somatic-mosaicism
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Feb 13, 2025 - R
Pipeline to process sc-ATAC data with pyCistopic
python bioinformatics pipeline nextflow atac-seq single-cell single-cell-atac-seq single-cell-multiomics multiome
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Oct 14, 2025 - Python
MSc Project - Integrative Analysis of Single-Nucleus RNA-Seq and ATAC-Seq of C9orf72 Knockout Mouse Brain
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Nov 21, 2024 - R
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