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omicverse/omicverse-skills

59 skills · 76 combined installs

Skills from this source

#
Skill
Source
8W Activity
Installs
1
omicverse-single-cell-clustering-backends Run and compare OmicVerse single-cell clustering backends as a reusable, triggerable skill. Use when choosing between…
omicverse/omicverse-skills
4
2
omicverse-single-cell-cellphonedb-communication Analyze single-cell cell-cell communication with OmicVerse CellPhoneDB and CellChat-style visualization. Use when con…
omicverse/omicverse-skills
3
3
omicverse-microbiome-16s-amplicon-dada2 16S rRNA amplicon analysis from raw FASTQs to a samples × ASVs AnnData with 7-rank SINTAX taxonomy, plus the canonica…
omicverse/omicverse-skills
2
4
omicverse-reference-label-transfer Transfer cell labels from a reference AnnData to a query AnnData with OmicVerse AnnotationRef. Use when converting Om…
omicverse/omicverse-skills
2
5
omicverse-single-cell-annotation Annotate single-cell AnnData with OmicVerse using the CellTypist, gpt4celltype, or SCSA branches. Use when turning Om…
omicverse/omicverse-skills
2
6
omicverse-single-cell-batch-integration Run OmicVerse single-cell batch integration as a reusable, triggerable skill after preprocessing is already complete.…
omicverse/omicverse-skills
2
7
omicverse-single-cell-cytotrace2 Predict single-cell developmental potency with OmicVerse CytoTRACE2 on AnnData. Use when converting an OmicVerse Cyto…
omicverse/omicverse-skills
2
8
omicverse-single-cell-differential-abundance Run OmicVerse single-cell differential abundance or compositional analysis as a reusable, triggerable skill. Use when…
omicverse/omicverse-skills
2
9
omicverse-single-cell-foundation-model Cell embedding, cell-type annotation, batch integration, and (where supported) perturbation prediction with single-ce…
omicverse/omicverse-skills
2
10
omicverse-single-cell-preprocessing Convert OmicVerse single-cell preprocessing and marker-discovery notebooks into a reusable, triggerable skill. Use wh…
omicverse/omicverse-skills
2
11
omicverse-single-cell-rna-velocity Analyze single-cell AnnData for RNA velocity with OmicVerse. Use when converting OmicVerse velocity notebooks into a …
omicverse/omicverse-skills
2
12
omicverse-single-cell-scenic Convert OmicVerse SCENIC notebooks into a reusable, triggerable skill for single-cell AnnData regulon analysis. Use w…
omicverse/omicverse-skills
2
13
omicverse-single-cell-sctour-trajectory Run the OmicVerse sctour trajectory branch on raw-count single-cell AnnData. Use when adapting the scTour part of an …
omicverse/omicverse-skills
2
14
omicverse-single-cell-trajectory-inference Run or adapt OmicVerse single-cell trajectory inference on cluster-ready AnnData. Use when converting OmicVerse traje…
omicverse/omicverse-skills
2
15
biocontext-knowledge-queries BioContext knowledge: UniProt, AlphaFold, STRING, Reactome, GO, PanglaoDB, PubMed, OpenTargets queries via ov.biocont…
omicverse/omicverse-skills
1
16
bulk-fastq-quantification End-to-end bulk RNA-seq quantification with omicverse's alignment module — SRA download, fastp QC, two interchangeabl…
omicverse/omicverse-skills
1
17
bulk-rna-seq-batch-correction-with-combat Bulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and…
omicverse/omicverse-skills
1
18
bulk-rna-seq-deconvolution-with-bulk2single Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fractio…
omicverse/omicverse-skills
1
19
bulk-rna-seq-deseq2-analysis-with-omicverse PyDESeq2 differential expression: ID mapping, DE testing, fold-change thresholding, and GSEA enrichment visualization…
omicverse/omicverse-skills
1
20
bulk-rna-seq-differential-expression-with-omicverse Bulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, volcano plots, and pathway enr…
omicverse/omicverse-skills
1
21
bulk-wgcna-analysis-with-omicverse WGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVe…
omicverse/omicverse-skills
1
22
bulktrajblend-trajectory-interpolation Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, tr…
omicverse/omicverse-skills
1
23
cellfate-pseudotime-gene-analysis CellFateGenie: Adaptive Threshold Regression for pseudotime-associated gene discovery, Mellon density, lineage scorin…
omicverse/omicverse-skills
1
24
data-export-excel Export analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM pr…
omicverse/omicverse-skills
1
25
data-export-pdf Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (…
omicverse/omicverse-skills
1
26
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_nano…
omicverse/omicverse-skills
1
27
data-stats-analysis Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and…
omicverse/omicverse-skills
1
28
data-transform Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Clau…
omicverse/omicverse-skills
1
29
data-viz-plots Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with AN…
omicverse/omicverse-skills
1
30
datasets-loading OmicVerse built-in datasets: pbmc3k, pancreas, dentategyrus, zebrafish, immune, spatial, multiome, plus create_mock_d…
omicverse/omicverse-skills
1
31
gsea-enrichment-analysis Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases an…
omicverse/omicverse-skills
1
32
omicverse-bulk-celltype-deconvolution Cell-type composition deconvolution of bulk RNA-seq using a single-cell reference. Wraps `ov.bulk.Deconvolution` with…
omicverse/omicverse-skills
1
33
omicverse-bulk-metabol-multivariate Multivariate discrimination and biomarker selection on a preprocessed metabolomics AnnData. Use when running PLS-DA, …
omicverse/omicverse-skills
1
34
omicverse-bulk-metabol-pathway-multifactor Pathway interpretation, multi-factor designs, differential correlation, MOFA multi-omics, and the MTBLS1 real-data ca…
omicverse/omicverse-skills
1
35
omicverse-bulk-metabol-preprocessing Run the canonical metabolomics preprocessing chain on an AnnData peak table — impute, normalize, transform — and appl…
omicverse/omicverse-skills
1
36
omicverse-bulk-metabol-untargeted-lipidomics Two adjacent LC-MS workflows on AnnData — (1) untargeted metabolomics with m/z-based peak annotation, mummichog pathw…
omicverse/omicverse-skills
1
37
omicverse-cross-modal-celltype-transfer Transfer cell-type labels from a reference AnnData to a query AnnData with OmicVerse weighted KNN over a shared embed…
omicverse/omicverse-skills
1
38
omicverse-micro-metabol-paired Paired microbiome × metabolomics integration on sample-aligned AnnDatas. Provides three methods - Spearman correlatio…
omicverse/omicverse-skills
1
39
omicverse-microbiome-da-comparison Run all three differential-abundance methods (Wilcoxon, pyDESeq2, ANCOM-BC) on the same microbiome AnnData, compare t…
omicverse/omicverse-skills
1
40
omicverse-microbiome-meta-analysis Combine multiple per-study microbiome AnnDatas into a single cross-cohort table and run inverse-variance / random-eff…
omicverse/omicverse-skills
1
41
omicverse-microbiome-phylogeny Build an ASV-level phylogenetic tree (MAFFT alignment + FastTree GTR+Γ), attach it to a 16S AnnData, and run phylogen…
omicverse/omicverse-skills
1
42
omicverse-single-cell-cellmatch-ontology Map free-text cell-type annotations to the Cell Ontology (CL) via NLP-based sentence-transformer matching, with optio…
omicverse/omicverse-skills
1
43
omicverse-single-cell-cellrank-fate CellRank fate maps from RNA velocity. Combine VelocityKernel + ConnectivityKernel into a transition matrix, fit a GPC…
omicverse/omicverse-skills
1
44
omicverse-single-cell-cellvote-consensus Multi-annotator consensus for single-cell labels via `ov.single.CellVote`. Combine labels from any subset of SCSA / g…
omicverse/omicverse-skills
1
45
omicverse-single-cell-differential-expression Run OmicVerse single-cell differential expression analysis as a reusable, triggerable skill. Use when comparing condi…
omicverse/omicverse-skills
1
46
omicverse-single-cell-kb-alignment Build a triggerable kb reference and quantify single-cell FASTQs with OmicVerse alignment.single. Use when converting…
omicverse/omicverse-skills
1
47
omicverse-single-cell-lda-topic-clustering Run OmicVerse single-cell LDA topic clustering with the MIRA backend as a reusable, triggerable skill. Use when fitti…
omicverse/omicverse-skills
1
48
omicverse-single-cell-liana-communication LIANA+ ligand-receptor inference on single-cell AnnData via `ov.single.run_liana`, plus the OmicVerse cell-cell commu…
omicverse/omicverse-skills
1
49
omicverse-single-cell-metatime-annotation Tumor microenvironment (TME) cell-state annotation via the pretrained MetaTiME meta-components (Yi et al. 2023). Thre…
omicverse/omicverse-skills
1
50
omicverse-single-cell-monocle2-trajectory Monocle2-style single-cell trajectory analysis on AnnData via the `ov.single.Monocle` class - DDRTree pseudotime + br…
omicverse/omicverse-skills
1
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