Starlitnightly
@Starlitnightly
Public Skills
fastq-analysis-pipeline
by Starlitnightly
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
single-cell-annotation-skills-with-omicverse
by Starlitnightly
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
single-cell-preprocessing-with-omicverse
by Starlitnightly
Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPUâGPU mixed, or GPU stacks.
data-transform
by Starlitnightly
Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
gsea-enrichment-analysis
by Starlitnightly
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
single-cell-clustering-and-batch-correction-with-omicverse
by Starlitnightly
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.
omicverse-visualization-for-bulk-color-systems-and-single-cell-d
by Starlitnightly
Guide users through OmicVerse plotting utilities showcased in the bulk, color system, and single-cell visualization tutorials, including venn/volcano charts, palette selection, and advanced embedding layouts.
data-viz-plots
by Starlitnightly
Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
data-export-pdf
by Starlitnightly
Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
data-export-excel
by Starlitnightly
Export analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
data-stats-analysis
by Starlitnightly
Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
bulktrajblend-trajectory-interpolation
by Starlitnightly
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
bulk-rna-seq-deseq2-analysis-with-omicverse
by Starlitnightly
Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.
single-cell-multi-omics-integration
by Starlitnightly
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
single-trajectory-analysis
by Starlitnightly
Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.
single-cell-downstream-analysis
by Starlitnightly
Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.
spatial-transcriptomics-tutorials-with-omicverse
by Starlitnightly
Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.
tcga-bulk-data-preprocessing-with-omicverse
by Starlitnightly
Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.
single2spatial-spatial-mapping
by Starlitnightly
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
bulk-rna-seq-differential-expression-with-omicverse
by Starlitnightly
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. Use when a user has bulk count matrices and needs differential expression analysis in omicverse.
bulk-wgcna-analysis-with-omicverse
by Starlitnightly
Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes.
string-protein-interaction-analysis-with-omicverse
by Starlitnightly
Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
bulk-rna-seq-deconvolution-with-bulk2single
by Starlitnightly
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.
single-cell-cellphonedb-communication-mapping
by Starlitnightly
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
bulk-rna-seq-batch-correction-with-combat
by Starlitnightly
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.