Anton Zhelonkin
Community@tony-zhelonkin · Chicago, Illinois
I`m a MD dermatologist, Computational Biology Postdoc at the University of Chicago. Exploring the gap between science and medicine
Agent Skills by Anton Zhelonkin
Showing 52 vetted skills indexed across 1 GitHub repositories.
tony-zhelonkinpycistarget-motif-enrichment
Run motif enrichment on scATAC-seq region sets with pycistarget to derive TF cistromes.
tony-zhelonkinscvi-basic
Perform unsupervised integration and batch correction for scRNA-seq data using scVI.
tony-zhelonkinbulk-rnaseq-pathway-explorer
Convert unified RNaseq results into standalone interactive HTML pathway dashboards.
tony-zhelonkinanndata
Read, write, subset, and concatenate AnnData objects in .h5ad format.
tony-zhelonkinanndatar-seurat-scanpy-conversion
Convert AnnData and Seurat objects between h5ad and R formats.
tony-zhelonkinscvi-framework
Route scvi-tools model selection and enforce shared data contracts across scvi-* models.
tony-zhelonkinscvi-scanvi
Transfer cell-type annotations in single-cell RNA-seq using scANVI from a trained scVI model.
tony-zhelonkintf-footprint-differential-analysis
Identify differential transcription factor occupancy from ATAC footprint analyses across conditions.
tony-zhelonkinscvi-peakvi
Analyze scATAC-seq data to generate batch-correct latent embeddings and differential accessibility.
tony-zhelonkinscvi-multivi
Integrate paired RNA and ATAC data into a shared latent embedding with cross-modality imputation.
tony-zhelonkincellranger-arc-multiome
Process Chromium Multiome ATAC+GEX data with cellranger-arc count.
tony-zhelonkinSKILL_IDENTIFIER
Initialize a modular AI research workflow template with YAML frontmatter.
tony-zhelonkinscvi-contrastivevi
Separate perturbation-specific from background variation in single-cell datasets.
tony-zhelonkinstarsolo-spliced-unspliced
Quantify spliced, unspliced, and ambiguous counts from FASTQ inputs using STARsolo Velocyto mode.
tony-zhelonkinpython-multimodal-10x
Run end-to-end multimodal single-cell RNA+ATAC analysis with Python tools.
tony-zhelonkinrna-velocity-trajectory
Infer directional cellular trajectories from scRNA-seq using spliced and unspliced RNA ratios.
tony-zhelonkinchromvar-motif-accessibility
Compute bias-corrected per-cell motif accessibility deviations from ATAC data.
tony-zhelonkinpycistopic-atac-topic-modeling
Identify co-accessible regulatory programs in scATAC-seq data using LDA topic modeling.
tony-zhelonkiniterative-peak-merging
Merge MACS2 summit peaks into fixed-width 501bp reference sets.
tony-zhelonkinseurat-multimodal-analysis
Consolidate multimodal single-cell RNA, protein, and chromatin data with Seurat and Signac.
tony-zhelonkinsingle-cell-rna-qc
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tony-zhelonkinscvi-scarches-reference-mapping
Map query datasets to reference atlases with scArches architectural surgery.
tony-zhelonkinscvi-hub-models
Load pretrained scvi-tools models from Hugging Face Hub for query-to-reference mapping.
tony-zhelonkinannotate-te-rnaseq-data
Annotate Ensembl IDs to gene symbols and parse TE identifiers from featureCounts outputs.