Source

smithery/Starlitnightly

23 skills · 0 combined installs

Skills from this source

#
Skill
Source
8W Activity
Installs
1
bulk-rna-seq-batch-correction-with-combat Bulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and…
smithery/Starlitnightly
0
2
bulk-rna-seq-deconvolution-with-bulk2single Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fractio…
smithery/Starlitnightly
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3
bulk-rna-seq-deseq2-analysis-with-omicverse PyDESeq2 differential expression: ID mapping, DE testing, fold-change thresholding, and GSEA enrichment visualization…
smithery/Starlitnightly
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4
bulk-rna-seq-differential-expression-with-omicverse Bulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, volcano plots, and pathway enr…
smithery/Starlitnightly
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5
bulk-wgcna-analysis-with-omicverse WGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVe…
smithery/Starlitnightly
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6
bulktrajblend-trajectory-interpolation Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, tr…
smithery/Starlitnightly
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7
data-export-excel Export analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM pr…
smithery/Starlitnightly
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8
data-export-pdf Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (…
smithery/Starlitnightly
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9
data-stats-analysis Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and…
smithery/Starlitnightly
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10
data-viz-plots Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with AN…
smithery/Starlitnightly
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11
gsea-enrichment-analysis Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases an…
smithery/Starlitnightly
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12
omicverse-visualization-for-bulk-color-systems-and-single-cell-d OmicVerse plotting: volcano, venn, boxplot, embedding, density, heatmap families, dotplot, convex hull, stacked bar, …
smithery/Starlitnightly
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13
single-cell-annotation-skills-with-omicverse Cell type annotation: SCSA, MetaTiME, CellVote consensus, CellMatch, GPTAnno, weighted KNN label transfer in OmicVers…
smithery/Starlitnightly
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14
single-cell-cellphonedb-communication-mapping CellPhoneDB v5 ligand-receptor analysis, CellChatViz plots, and the newer ccc_heatmap / ccc_network_plot / ccc_stat_p…
smithery/Starlitnightly
0
15
single-cell-clustering-and-batch-correction-with-omicverse Single-cell clustering (Leiden, Louvain, scICE, GMM), batch correction (Harmony, scVI, BBKNN, Combat), topic modeling…
smithery/Starlitnightly
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16
single-cell-downstream-analysis AUCell pathway scoring, metacell DEG, scDrug response, SCENIC regulons, cNMF programs, and NOCD community detection i…
smithery/Starlitnightly
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17
single-cell-multi-omics-integration Multi-omics integration: MOFA factor analysis, GLUE unpaired alignment, SIMBA batch correction, TOSICA label transfer…
smithery/Starlitnightly
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18
single-cell-preprocessing-with-omicverse Single-cell QC, normalization, HVG detection, PCA, neighbor graph, UMAP/tSNE embedding pipelines in OmicVerse (CPU/GP…
smithery/Starlitnightly
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19
single-trajectory-analysis Trajectory & RNA velocity: PAGA, Palantir, VIA, dynamo, scVelo, latentvelo, graphvelo backends via ov.single.Velo. Ps…
smithery/Starlitnightly
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20
single2spatial-spatial-mapping Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest t…
smithery/Starlitnightly
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21
spatial-transcriptomics-tutorials-with-omicverse Spatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tang…
smithery/Starlitnightly
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22
string-protein-interaction-analysis-with-omicverse STRING protein-protein interaction network analysis with pyPPI: query STRING database, build PPI graphs, expand with …
smithery/Starlitnightly
0
23
tcga-bulk-data-preprocessing-with-omicverse TCGA bulk RNA-seq preprocessing with pyTCGA: GDC sample sheets, expression archives, clinical metadata, Kaplan-Meier …
smithery/Starlitnightly
0