pseudobulking on an AnnData object
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Jun 17, 2026 - Python
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pseudobulk
Here are 9 public repositories matching this topic...
Snakemake pipeline for scATAC-seq pseudobulk replicate creation
bioinformatics snakemake pipeline genomics genetics biology epigenetics cells atac-seq bam single-cell molecular-biology scatac-seq pseudobulk sinto
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Apr 5, 2026 - Python
Donor-level astrocyte lncRNA analysis: a replicated Alzheimer's disease signature that is inverted in ALS (Brain Research revision, single-author, Hidenori Tani, Yokohama University of Pharmacy)
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Aug 6, 2026 - Python
End-to-end reproducible R/Bioconductor pipeline for donor-aware paired single-cell RNA-seq analysis featuring QC, clustering, pseudobulk differential expression, functional enrichment, and automated reporting.
bioinformatics genomics rstats bioconductor transcriptomics reactome edger single-cell-rna-seq singlecellexperiment pseudobulk go-enrichment
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Aug 7, 2026 - HTML
Archived version – superseded by updated dual implementation repository.
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Jan 10, 2026 - Jupyter Notebook
Pseudobulk and metacell aggregation for single-cell RNA-seq (AnnData/scanpy + Seurat/R)
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Jun 7, 2026 - Python
Cross-cohort benchmarking of frozen Geneformer and expression pseudobulk for donor-level SLE classification
single-cell-rna-seq pseudobulk systemic-lupus-erythematosus geneformer cross-cohort-transfer bioinformatics-benchmark
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Jul 27, 2026 - Python
Scripts and data for used in the TE Aging Manuscript
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Sep 23, 2025 - R
gSWITCH: A tool for identifying switch genes in biological network
bioinformatics time-series single-cell-rna-seq bulk-rna-seq gswitch pseudobulk switch-genes lineage-progression veriable-dependent-changes
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Aug 9, 2026 - R
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