Search Results: omicverse

Found 9 Skills

single-cell-clustering-and-batch-correction-with-omicverse

Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.

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Data Processingstarlitnightly/omicverse

single-cell-preprocessing-with-omicverse

Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.

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Data Processingstarlitnightly/omicverse

tcga-bulk-data-preprocessing-with-omicverse

Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.

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Data Processingstarlitnightly/omicverse

single-cell-cellphonedb-communication-mapping

Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.

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Data Processingstarlitnightly/omicverse

bulk-rna-seq-deconvolution-with-bulk2single

Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.

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Data Processingstarlitnightly/omicverse

single2spatial-spatial-mapping

Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.

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Data Processingstarlitnightly/omicverse

bulk-wgcna-analysis-with-omicverse

Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes.

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Data Processingstarlitnightly/omicverse

bulk-rna-seq-deseq2-analysis-with-omicverse

Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.

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Data Processingstarlitnightly/omicverse

single-cell-annotation-skills-with-omicverse

Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.

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