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…
Skills
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Updated 11-05 00:16
Data & analytics
17,404 results
bulk-rna-seq-deseq2-analysis-with-omicverse
PyDESeq2 differential expression: ID mapping, DE testing, fold-change thresholding, and GSEA enrichment visualization in OmicVerse.
bulk-wgcna-analysis-with-omicverse
WGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVerse.
bulktrajblend-trajectory-interpolation
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and…
data-io-loading
OmicVerse data I/O: use ov.read(), ov.io.read_h5ad, read_10x_h5, read_10x_mtx, read_visium, read_visium_hd, read_nanostring instead of scanpy. Covers h5ad,…
data-stats-analysis
Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider…
data-transform
Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
data-viz-plots
Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with ANY LLM provider.
datasets-loading
OmicVerse built-in datasets: pbmc3k, pancreas, dentategyrus, zebrafish, immune, spatial, multiome, plus create_mock_dataset() and predefined_signatures GMT…
gsea-enrichment-analysis
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
omicverse-cross-modal-celltype-transfer
Transfer cell-type labels from a reference AnnData to a query AnnData with OmicVerse weighted KNN over a shared embedding. Use when converting OmicVerse…
omicverse-microbiome-da-comparison
Run all three differential-abundance methods (Wilcoxon, pyDESeq2, ANCOM-BC) on the same microbiome AnnData, compare their hit sets via 3-way Venn / overlap…
omicverse-single-cell-cellvote-consensus
Multi-annotator consensus for single-cell labels via `ov.single.CellVote`. Combine labels from any subset of SCSA / gpt4celltype / GPTBioInsightor / scMulan /…
omicverse-single-cell-kb-alignment
Build a triggerable kb reference and quantify single-cell FASTQs with OmicVerse alignment.single. Use when converting OmicVerse alignment notebooks into a…
omicverse-single-cell-lda-topic-clustering
Run OmicVerse single-cell LDA topic clustering with the MIRA backend as a reusable, triggerable skill. Use when fitting topic models on count-like AnnData,…
omicverse-single-cell-liana-communication
LIANA+ ligand-receptor inference on single-cell AnnData via `ov.single.run_liana`, plus the OmicVerse cell-cell communication (CCC) plotting stack with…
omicverse-single-cell-monocle2-trajectory
Monocle2-style single-cell trajectory analysis on AnnData via the `ov.single.Monocle` class - DDRTree pseudotime + branch detection + per-gene differential…
omicverse-visualization-for-bulk-color-systems-and-single-cell-d
OmicVerse plotting: volcano, venn, boxplot, embedding, density, dotplot, convex hull, stacked bar, and Forbidden City color palettes.
spatial-transcriptomics-tutorials-with-omicverse
Spatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tangram, cell2location, Starfysh), clustering…
string-protein-interaction-analysis-with-omicverse
STRING protein-protein interaction network analysis with pyPPI: query STRING database, build PPI graphs, expand with add_nodes, and visualize styled networks…
tcga-bulk-data-preprocessing-with-omicverse
TCGA bulk RNA-seq preprocessing with pyTCGA: GDC sample sheets, expression archives, clinical metadata, Kaplan-Meier survival analysis, and annotated AnnData…
0xarchive
Query historical crypto market data from 0xArchive across Hyperliquid, Lighter.xyz, and HIP-3. Covers orderbooks, trades, candles, funding rates, open…
financial-market-analysis
Precision Financial Insights - Analyze stocks, companies, and market sentiment using authoritative data. Powered by Yahoo Finance and enhanced with intelligent…
gdpr-dsgvo-expert
GDPR and German DSGVO compliance automation. Scans codebases for privacy risks, generates DPIA documentation, tracks data subject rights requests. Use for GDPR…