Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Assemble ONT/HiFi reads with Flye/Hifiasm, polish with Medaka, QC with QUAST/BUSCO, call SVs (DEL/INS/INV/DUP/BND) with Sniffles2. Use for long-read assembly, N50/BUSCO QC, or nanopore/HiFi SV calling to VCF.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Fit Bayesian models with PyMC/Bambi/ArviZ: NUTS sampling, prior/posterior checks, HDI intervals, hierarchical GLMMs, LOO/WAIC comparison. Use when doing Bayesian inference, hierarchical modeling, or MCMC diagnostics.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Parse/write FASTA, FASTQ, SAM/BAM, VCF, BED, GFF/GTF with pysam and pure Python; decode SAM FLAG/CIGAR; reconcile 0-based vs 1-based coordinates. Use for custom format parsers or off-by-one coordinate bugs.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Fit Michaelis-Menten Vmax/Km with scipy curvefit, convert absorbance to concentration via Beer-Lambert, and model enzyme inhibition. Use when analyzing enzyme assays or estimating Km, Vmax, kcat, or Ki.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Classify tumor RNA-seq into subtypes (melanoma Tirosh/Harbst on TCGA-SKCM): log1p/z-score, PCA/t-SNE, hierarchical clustering, random forest, Kaplan-Meier survival. Use when subtyping cBioPortal expression data.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
BLAST-identify unknown DNA/CDS with Biopython, QC/translate sequences, build NJ/UPGMA trees, and scan protein motifs. Use for sequence-to-discovery capstones, unknown-sequence ID, or FASTA-BLAST-tree pipelines.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Annotate scRNA-seq Leiden/Louvain clusters into cell types via canonical marker scoring, SingleR reference correlation, and CellTypist logistic-regression classification on an AnnData/SingleCellExperiment object. Use when doing cell type annotation, labeling clusters, scoring marker genes on a UMAP, running SingleR or…
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
FASTQ-to-peaks ChIP-seq pipeline: Bowtie2 align, Picard dedup, MACS2/MACS3 narrow/broad peak calling, FRiP/IDR QC, deepTools bamCoverage/heatmaps. Use for ChIP-seq/CUT&RUN peak calling or FRiP/NRF/IDR QC.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Normalize CITE-seq ADT counts (CLR/DSB) and build WNN graphs joining RNA+protein or RNA+ATAC with muon/Seurat FindMultiModalNeighbors. Use for CITE-seq, 10x Multiome, or paired RNA+ADT/ATAC single-cell integration.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Classify germline variant pathogenicity with ACMG/AMP 5-tier criteria (PVS1/PS1-4/PM1-6/PP1-5/BA1/BS1-4/BP1-7), query ClinVar via NCBI E-utilities, and filter by gnomAD population frequency to draft a clinical variant report. Use when doing ACMG classification, deciding Pathogenic/Likely Pathogenic/VUS/Likely…
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Call CNVs from binned read-depth: GC-bias normalization, circular binary segmentation (CBS), log2-ratio-to-CN-state calling, tumor-purity correction. Use for CNV/copy-number segmentation, log2 ratio analysis, or gain/deletion/amplification calls.
Pavel-Kravchenko/Bioinformatics
Skill Claude CodeCodex
Generate normalized bigWig coverage tracks from BAM with deepTools bamCoverage/bamCompare (RPKM/CPM/RPGC), summarize with multiBamSummary, and plot TSS/region signal with computeMatrix + plotHeatmap/plotProfile; pyBigWig for programmatic access. Use when normalizing BAM to bigWig, computing ChIP/input log2 ratio…