LIANA: a LIgand-receptor ANalysis frAmework
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Aug 7, 2024 - R
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cellchat
Here are 22 public repositories matching this topic...
A comprehensive computational pipeline that bridges single-cell genomics and cheminformatics to accelerate Alzheimer's Disease research. This project integrates advanced bioinformatics and machine learning to create a seamless workflow from raw single-cell RNA sequencing data to predictive drug discovery models.
python flask machine-learning bioinformatics rna-seq r cheminformatics bioinformatics-pipeline drug-discovery single-cell alzheimers-disease qsar-models cellchat milor qsar-modeling
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Jul 13, 2025 - Jupyter Notebook
Generate Sankey plots from merged CellChat objects
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Jan 21, 2025
This project analyzes how differences in the mathematical frameworks of CellChat and CellPhoneDB affect cell–cell communication inference from single-cell RNA-seq data in diet-induced liver disease.
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Jun 8, 2026 - Jupyter Notebook
Modular single-cell transcriptomics pipelines for Alzheimer’s disease, integrating R and Python workflows.
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Jan 14, 2026 - R
Customize your specific organism cellchatdb
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Feb 20, 2024 - R
A geometry-aware framework for prioritizing biologically meaningful ligand–receptor interactions in spatial transcriptomics.
bioinformatics reproducible-research computational-biology cancer-genomics spatial-transcriptomics tumor-microenvironment ligand-receptor cell-cell-communication cellchat spatial-biology
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Jun 23, 2026 - Jupyter Notebook
Spatial transcriptomics analysis of macrophages in chronic kidney disease (CKD): cell2location deconvolution, CellChat cell-cell communication, differential expression and co-expression analysis (Python/R).
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Aug 5, 2026 - Jupyter Notebook
Single-cell RNA-seq analysis of human bone marrow and CD34+ cells using Seurat, SingleR, DoubletFinder and CellChat.
bioinformatics scrna-seq r-language single-cell-rna-seq seurat bone-marrow singler cellchat doubletfinder
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Jul 10, 2026 - R
Reproducible R analysis code for fibroblast FLRT2–UNC5C signalling in human obese HFpEF (single-nucleus + orthogonal-bulk, CellChat)
bioinformatics transcriptomics heart-failure cell-cell-communication cellchat hfpef single-nucleus-rna-seq cardiac-fibroblast flrt2 unc5c
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Jun 27, 2026 - R
Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
python bioinformatics r sequencing velocity epigenetics rna transcriptome single-cell pathway-analysis gsea regeneration seurat rna-velocity single-nuclei-rna-sequencing single-nuclei cellchat single-cell-rna-sequencing retinal-ganglion-cell optic-nerve-crush
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Jun 24, 2024 - R
Code-only downstream scRNA-seq workflows for PBMC and colorectal cancer analyses, with reproducible entry points and expected output structure.
workflow bioinformatics reproducible-research scrna-seq transcriptomics single-cell-rna-seq scanpy cellchat
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Mar 17, 2026 - Python
Spatial transcriptomics analysis of paired baseline and on-treatment samples using Seurat and CellChat
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Jun 9, 2026 - R
Single-nucleus RNA-seq analysis of FLC samples generated by the Khashayar lab, including QC, harmony integration, and CellChat analysis
harmony bioinformatics rna-seq r scrna-seq single-cell seurat tumor-microenvironment cellchat cancer-biology fibrolamellar-carcinoma
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Apr 21, 2026
可视化2026718V1：离线科研图形决策、Scheme/Recipe 检索、R/Python 适配渲染与科学视觉复核
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Jul 24, 2026 - Python
End-to-end single-cell RNA-seq analyses on public datasets — 10 reproducible projects in Scanpy & Seurat covering integration, trajectory inference, cell-cell communication, and method benchmarks.
harmony bioinformatics integration reproducible-research benchmarks breast-cancer scrnaseq palantir single-cell-rna-seq glioblastoma melanoma hematopoiesis batch-correction single-cell-analysis seurat trajectory-inference scanpy scvelo colorectal-cancer cellchat
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Jun 2, 2026 - Jupyter Notebook
Growth Hormone effect on Cartilage Growth Plate; Light-Sheet Microscopy; Pseudocoloring | Projects I started and still working on in Andrei Chagin Lab | Karolinska Institutet
python r velocity rna single-cell bone seurat light-sheet-microcopy pseudocolor rna-velocity cartilage stem-cells cellchat
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Aug 18, 2023 - Jupyter Notebook
Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital
python r velocity rna transcriptomics single-cell forceatlas2 seurat microglia scanpy macrophage rna-velocity scvelo cellchat oir socs3 spp1 gobp
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Dec 16, 2023 - Jupyter Notebook
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