Pavel-Kravchenko/Bioinformatics

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Assign SARS-CoV-2 Pango lineages with Pangolin/Nextclade and deconvolve wastewater into lineage fractions with Freyja (variants/demix). Use when doing variant surveillance, wastewater epidemiology, lineage tracking, or VOC/VOI classification.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Compute TCR/BCR clonotype diversity (Shannon, Simpson, clonality, Chao1, D50) from AIRR/10x VDJ tables; explains IMGT V/D/J nomenclature and CDR3 junctions. Use for repertoire diversity, clonal expansion, or scTCR-seq analysis.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Assemble viral genomes from ARTIC amplicon FASTQ with minimap2/iVar/LoFreq; call consensus, detect quasispecies variants. Use when doing SARS-CoV-2/HIV/Influenza assembly, ARTIC pipelines, or minority variant calling.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Dock ligand libraries with AutoDock Vina/meeko, filter hits by ADMET (Lipinski, LogS, hERG), rank by composite docking+QSAR score in pandas. Use when docking SMILES/SDF vs a target or prioritizing virtual screening hits.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Align WGBS/RRBS bisulfite FASTQ with Bismark, extract per-CpG methylation into beta/M-values. Use for bismarkgenomepreparation, deduplicatebismark, bismarkmethylationextractor, or bismark.cov/CpGreport analysis.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Write Snakemake rules/wildcards/config and Nextflow DSL2 processes/channels; run nf-core pipelines (rnaseq, sarek) on SLURM/AWS/GCP. Use when building a Snakefile, DSL2 workflow, or nf-core samplesheet.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Fetch sequences via NCBI Entrez (esearch/efetch/elink), UniProt REST, and RCSB PDB APIs with BioPython/urllib. Use when picking a database, decoding accession prefixes (NM/XM/GSE/SRR), or cross-linking a gene NCBI-UniProt-PDB.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Manipulate Seq/SeqRecord objects, parse FASTA/FASTQ/GenBank with SeqIO, query NCBI via Entrez, and run PairwiseAligner in Biopython. Use for sequence I/O, translation, reverse complement, GC content, or NCBI fetch in Python.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Search protein/nucleotide sequences for homologs with NCBI BLAST+ (blastp/blastn/blastx/tblastn) via Biopython qblast or a local blastdb; parse E-value/bit-score/identity. Use for BLAST search, homology/similarity search, or FASTA annotation.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Parse Sanger .ab1/.abi chromatograms with BioPython, extract Phred quality/trace channels, plot traces, quality-trim, and flag het double-peaks. Use for .ab1/.scf files or detecting het SNPs/mixed peaks.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build dot plots, detect synteny/rearrangements, classify orthologs vs paralogs, compute pan-genomes; pick MUMmer/LASTZ/minimap2 for alignment. Use when comparing genomes, reading a dot plot, or finding synteny/orthologs.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Translate DNA per-frame, score codon usage bias (RSCU/CAI), simulate restriction digests/ORFs, and test three-point-cross mapping and Hardy-Weinberg equilibrium. Use for CAI, virtual digests, crossover mapping, or HWE tests.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build/scan PWMs (PPM, log-odds, info content, logos) for DNA motifs, convert PROSITE patterns to regex, parse HMMER domtblout/Pfam hits. Use for TF binding scans, promoter motifs, PROSITE matches, or Pfam/InterPro domain mapping.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Decode GO evidence codes (IDA/IEA/TAS), propagate GO annotations via the true path rule, and run ORA (hypergeometric test + BH-FDR) in Python/R. Use when doing GO enrichment, evidence-code checks, or DAG annotation propagation.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Analyze Hi-C contact matrices with cooler/cooltools: load .cool/.mcool files, visualize contact maps, compute P(s) decay curves, call A/B compartments (eigenvector), detect TAD boundaries (insulation score), and build pileups. Use when working with Hi-C data, chromatin conformation capture, 3D genome organization…

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build PFM/PPM/PWM from TF binding sites, score/scan DNA with NumPy, pick thresholds, test motif enrichment (Fisher/BH-FDR). Use for ChIP-seq/SELEX motif scoring, IUPAC consensus, or JASPAR/HOCOMOCO matching.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Align FASTA sequences via MAFFT/MUSCLE/Clustal Omega, parse with Biopython AlignIO, build UPGMA guide trees, score sum-of-pairs/consensus/conservation. Use for MSA, MSA tool choice, consensus/logo, or guide-tree building.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Compute DNA helix geometry (A/B/Z-DNA), nearest-neighbor duplex free energy (SantaLucia), and RNA dot-bracket structure/Nussinov folding with Biopython. Use when analyzing helix groove geometry, oligo Tm/stability, or RNA stem-loop/hairpin structure.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Align two protein/DNA sequences with Biopython's PairwiseAligner (global Needleman-Wunsch, local Smith-Waterman), BLOSUM/PAM substitution matrices, and affine gap penalties; compute percent identity/similarity and E-values. Use when doing pairwise sequence alignment, ortholog comparison, dot plots, or choosing…

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Run GO/KEGG pathway enrichment via ORA (hypergeometric test) or GSEA, with BH-FDR and KEGG REST API queries. Use for "GO enrichment", "GSEA", "ORA vs GSEA", or "pathway enrichment" requests.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build NJ/UPGMA trees from aligned FASTA with BioPython Bio.Phylo, score p-distance/JC69/K2P models, and parse Newick with bootstrap support. Use for tree building from an MSA, Newick I/O, or bootstrap-value interpretation.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Parse PDB files with BioPython Bio.PDB, compute distance/angle/dihedral/RMSD, superimpose structures (Kabsch), assign DSSP secondary structure. Use for protein structure analysis, RMSD/alignment, contact maps, Ramachandran plots.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build PFM/PPM/PWM matrices from aligned sites with NumPy, scan sequences on both strands, compute information content, plot sequence logos, convert PROSITE patterns to regex. Use for motif scanning, TF binding site scoring, or PROSITE-to-regex tasks.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build reproducible, resumable bioinformatics pipelines with Snakemake rules or Nextflow DSL2 processes, run nf-core pipelines, and add pytest unit tests plus GitHub Actions CI. Use when writing a Snakefile, defining Nextflow processes/channels, scaling a pipeline to SLURM/AWS/GCP, containerizing tools with…