Analysis notebooks supporting snPATHO-Seq for single-nucleus RNA profiling of archival FFPE tissue.
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Sep 24, 2022 - Jupyter Notebook
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single-nucleus-rna-seq
Here are 6 public repositories matching this topic...
Analysis and figure-regeneration code for a two-cohort early-onset Alzheimer's disease transcriptomic study with matched-null testing and cross-layer evaluation.
bioinformatics meta-analysis reproducibility transcriptomics colocalization mendelian-randomization single-nucleus-rna-seq early-onset-alzheimers-disease matched-null-testing
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Aug 4, 2026 - R
Human kidney healthy & injured cell-state atlas (Lake et al. Nature 2023) — computational reproduction: sn/scRNA-seq · Visium · Slide-seq · KPMP niches. Colab-ready notebook for multi-omics & spatial figure reanalysis.
machine-learning bioinformatics systems-biology jupyter-notebook computational-biology kidney single-cell nature multi-omics chronic-kidney-disease google-colab seurat spatial-transcriptomics nephrology scanpy cell-atlas visium slide-seq single-nucleus-rna-seq kpmp
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Jul 7, 2026 - Jupyter Notebook
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
Kidney papilla Visium + snRNA-seq reproduction (Canela et al. Nat Commun 2023): label transfer · stone vs control spatial DE · mineralization ROI. GEO GSE206306/GSE231569 · RunPod/Colab ready.
machine-learning bioinformatics geo systems-biology jupyter-notebook computational-biology kidney single-cell multi-omics google-colab spatial-transcriptomics nephrology scanpy visium spatial-omics runpod label-transfer nature-communications kidney-stone single-nucleus-rna-seq
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Jul 1, 2026 - Python
Single-nucleus transcriptomic profiling of cortical SST+ GABAergic interneurons in Alzheimer's disease to resolve selective metabolic vulnerability, modeling the pathogenic collapse of the PPARGC1A mitochondrial biogenesis regulon against SATB1-mediated cell-identity homeostasis.
differential-expression pathway-enrichment-analysis neurodegeneration gene-regulatory-networks gabaergic-neurons single-nucleus-rna-seq somatostatin-interneurons alzheimers-pathology selective-vulnerability mitochondrial-biogenesis ppargc1a-regulon satb1-chromatin transcriptional-collapse cortical-microcircuitry bioenergetic-failure snrna-seq-pipeline hypergeometric-ora regulon-activity-scoring
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Jun 25, 2026 - Python
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