Pavel-Kravchenko/Bioinformatics

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Design PCR/qPCR primers with primer3-py designprimers/calchairpin, Bio.SeqUtils Tm, and blastn specificity checks. Use when designing PCR, qPCR, cloning, or genotyping primers, or checking Tm/dimers/specificity.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Detect TATA box/Inr/DPE promoter elements, call CpG islands (O/E ratio), and build/score PWMs for TFBS scanning. Use when finding a TATA box, calling CpG islands, or scanning a sequence for transcription factor binding sites.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Compute peptide b/y ion masses, run trypsin/PMF search, quantify LFQ protein abundance (volcano plots), and calculate PTM shifts and protein inference. Use for MS/MS peptide ID, PMF search, LFQ quantification, or PTM analysis.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Run QIIME2 16S amplicon workflows: import FASTQ, DADA2 denoise to ASVs, SILVA taxonomy, alpha/beta diversity, ANCOM-BC. Use when analyzing 16S/amplicon microbiome data or .qza/.qzv pipelines.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build QSAR classifiers from ChEMBL IC50 data with RDKit Morgan fingerprints, Random Forest, scaffold splits, and k-NN applicability domain. Use when predicting activity/pIC50 from SMILES or building structure-activity relationship models.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Parse SMILES with RDKit, compute MW/LogP/TPSA/HBD/HBA descriptors and Lipinski Ro5, build Morgan/ECFP4 and MACCS fingerprints, score Tanimoto similarity. Use for cheminformatics, drug-likeness screening, or fingerprint similarity search.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Scan DNA for promoter/regulatory elements: TATA box regex search, CpG island detection via GC%/observed-over-expected sliding windows, and PFM to PWM (log-odds) construction/scanning for TFBS. Use when locating a TSS, calling CpG islands, building a position weight matrix from aligned binding sites, or scanning a…

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Ribo-seq: cutadapt/bowtie2 adapter+rRNA removal, plastid P-site calibration, 3-nt periodicity QC, RiboCode/ribotricer ORF calling, translation efficiency. Use when user has ribosome profiling or footprint data.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Bulk RNA-seq — STAR/HISAT2/featureCounts or Salmon/kallisto quantification, TPM/DESeq2 size-factor normalization, DESeq2/pydeseq2 DE testing. Use for RNA-seq design, count matrices, or DE analysis with DESeq2, edgeR, pydeseq2.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Correct batch effects and integrate multiple scRNA-seq AnnData datasets with Harmony (harmonypy), scVI, or BBKNN; quantify mixing with LISI/ASW/kBET and transfer cell-type labels via KNN or scANVI. Use when merging samples from different batches/donors/labs/10x runs, when a UMAP shows batch-driven clustering instead…

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

TF-IDF normalize scATAC-seq peak matrices and run LSI/SVD, dropping depth-correlated component 1, via SnapATAC2 or Signac/Seurat. Use when clustering 10x fragments.tsv.gz, running LSI/UMAP on ATAC data, or linking peaks to genes.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Compute Gini index and replicate LFC correlation on CRISPR sgRNA count matrices; apply DESeq2-style median-ratio normalization before MAGeCK/CRISPRcleanR. Use when QC'ing a CRISPR screen count table or flagging copy-number-biased dropout.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build AnnData from 10x MEX, compute scanpy QC (pctcountsmt, ngenesbycounts), MAD-filter cells, normalize/log1p, select HVGs. Use for scRNA-seq preprocessing, doublet/dying-cell filtering, or AnnData QC before clustering.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Run a full scRNA-seq analysis in scanpy on an AnnData/10x/h5ad matrix — QC filtering (pctcountsmt, ngenesbycounts), normalizetotal/log1p, HVG selection, PCA, neighbors/UMAP, Leiden clustering, and rankgenesgroups marker detection. Use when processing single-cell RNA-seq count matrices, clustering cells, annotating…

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

SNP calling pipeline: Trimmomatic trim, BWA-MEM2/HISAT2 align, samtools mpileup + bcftools call, ANNOVAR annotate (dbSNP, RefGene, 1000G, ClinVar). Use for FASTQ-to-VCF pipelines or ANNOVAR variant annotation.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Analyze Visium/Xenium/MERFISH spatial transcriptomics with Squidpy/Scanpy: QC, spatial neighbor graphs, Moran's I spatially variable genes, tissue-image plots. Use for spatial autocorrelation or SVG detection.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Run t-test/Mann-Whitney/ANOVA with scipy.stats, apply Bonferroni/BH-FDR via statsmodels, compute Cohen's d and power. Use for comparing expression/counts between groups, correcting p-values, or genomics power analysis.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Parse PDB CRYST1/header for unit cell, space group, resolution, R-factors; apply symmetry operators; pick X-ray vs cryo-EM vs NMR. Use when checking structure quality, parsing CRYST1, or choosing a method.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Classify shotgun metagenome reads to species level with Kraken2, remove host reads with Bowtie2, and re-estimate abundance with Bracken. Use when doing metagenomics taxonomic profiling, Kraken2/Bracken, or host decontamination workflows.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Write pytest tests/fixtures for bio functions and GitHub Actions CI with pytest-cov, ruff, black, mypy. Use when adding tests to a bio tool, writing conftest.py fixtures, or building tests.yml/lint.yml CI workflows.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Detect TF footprints in ATAC-seq via Tn5 offset correction, insertion-profile aggregation, footprint scoring, and pybedtools intersect/slop/closest. Use when doing TF footprinting, ATAC-seq Tn5 bias correction, footprint scoring, or motif-site meta-profile plots.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Order scRNA-seq cells with diffusion pseudotime (scanpy sc.tl.dpt), PAGA graphs, and RNA velocity (scVelo) on spliced/unspliced counts. Use for pseudotime, root cell selection, or RNA velocity streamline plots.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Annotate a VCF's consequence/HGVS/impact with Ensembl VEP or snpEff, then join gnomAD AF, ClinVar, and dbNSFP scores. Use when annotating a VCF, running VEP/snpEff, or parsing CSQ/ANN fields.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Run GATK/bcftools BAM-to-VCF calling, parse VCF fields, decode genotypes (GT/AD/DP/GQ), hard-filter variants, test Hardy-Weinberg equilibrium. Use for SNP/indel calling, VCF/GVCF parsing, zygosity decoding, or HWE checks.