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Claude Skills by Pavel-Kravchenko
github.com/Pavel-Kravchenko213 skills0 installs219 views
- Bio Applied Rna Seq AnalysisRNA-seq workflow — experimental design, alignment vs pseudo-alignment, count normalization (TPM), differential expression setup, and key pitfallsVotes: 0GitHub stars: 4
- Bio Applied Sc IntegrationSingle-Cell Batch Correction and Dataset Integration with NumPyVotes: 0GitHub stars: 4
- Bio Applied Scatac ChromatinSingle-Cell ATAC-seq: Chromatin Accessibility with NumPyVotes: 0GitHub stars: 4
- Bio Applied Screen Qc NormalizationCRISPR screen quality control and normalization: library distribution QC, Gini index, replicate correlation, and count normalization. Use when processing CRISPR screen count matrices.Votes: 0GitHub stars: 4
- Bio Applied Scrna PreprocessingscRNA-seq QC and preprocessing: AnnData construction, QC metrics, MAD filtering, normalization strategiesVotes: 0GitHub stars: 4
- Bio Applied Single Cell ScanpyFull scanpy scRNA-seq workflow: QC, normalization, HVG, PCA, UMAP, Leiden clustering, marker gene detectionVotes: 0GitHub stars: 4
- Bio Applied Snp Calling PipelineSNP calling pipeline: Trimmomatic, HISAT2/BWA-MEM2 alignment, samtools/bcftools variant calling, ANNOVAR annotationVotes: 0GitHub stars: 4
- Bio Applied Spatial TranscriptomicsSpatial transcriptomics: Visium data loading, spatial QC, spatial neighbor graphs, Moran's I for spatially variable genes, tissue visualization with SquidpyVotes: 0GitHub stars: 4
- Bio Applied Statistics For BioinformaticsStatistical testing for bioinformatics: distributions, hypothesis testing, multiple testing correction (Bonferroni, BH/FDR), parametric vs non-parametric test selectionVotes: 0GitHub stars: 4
- Bio Applied Structural MethodsProteomics and structural methods: mass spectrometry ionization, MS/MS b/y ion calculation, trypsin digestion, database search engines, peptide mass fingerprintingVotes: 0GitHub stars: 4
- Bio Applied Taxonomic ProfilingTaxonomic profiling of shotgun metagenomes: host decontamination, Kraken2 classification, Bracken abundance re-estimationVotes: 0GitHub stars: 4
- Bio Applied Testing CicdTesting and CI/CD for bioinformatics: pytest patterns, fixtures, GitHub Actions workflows, bioinformatics-specific test strategiesVotes: 0GitHub stars: 4
- Bio Applied Tf FootprintingTF footprinting from ATAC-seq — Tn5 insertion profiles, footprint score calculation, pybedtools interval operations, accumulation plots.Votes: 0GitHub stars: 4
- Bio Applied Trajectory AnalysisscRNA-seq trajectory analysis: pseudotime (DPT), PAGA graph abstraction, and RNA velocity (scVelo). Decision guide, key parameters, and pitfalls.Votes: 0GitHub stars: 4
- Bio Applied Variant Calling And Snp AnalysisVariant calling pipeline, VCF format, genotype decoding, and SNP analysis with GATK/bcftoolsVotes: 0GitHub stars: 4
- Bio Applied Variant SurveillanceSARS-CoV-2 lineage classification (Pango), Freyja wastewater deconvolution, spike protein mutation tracking, and surveillance pipeline toolsVotes: 0GitHub stars: 4
- Bio Applied Vdj BiologyV(D)J Recombination and Adaptive Immune ReceptorsVotes: 0GitHub stars: 4
- Bio Applied Viral Genome AssemblyViral genome assembly pipeline — ARTIC amplicon sequencing, iVar/LoFreq variant calling, quasispecies/minority variant detection, QC thresholds, and key pitfallsVotes: 0GitHub stars: 4
- Bio Applied Virtual ScreeningVirtual screening for drug discovery: pharmacophore modeling, docking score filtering, and ADMET prediction. Use when computationally screening compound libraries.Votes: 0GitHub stars: 4
- Bio Applied Wgbs BismarkWGBS/RRBS Processing with Bismark with BismarkVotes: 0GitHub stars: 4
- Bio Applied Workflow EnginesSnakemake and Nextflow/nf-core workflow patterns for genomics pipelines — rules, wildcards, config, cluster execution, and comparison table.Votes: 0GitHub stars: 4
- Bio Core Biological DatabasesProgrammatic access to NCBI (Entrez), UniProt, GEO, and SRA — accession types, API patterns, rate limits, and cross-database linking with BioPythonVotes: 0GitHub stars: 4
- Bio Core Biopython EssentialsBioPython essentials — Seq/SeqRecord objects, SeqIO file I/O, Entrez API, pairwise alignment with PairwiseAligner.Votes: 0GitHub stars: 4
- Bio Core Blast SearchingBLAST: Sequence Similarity Searching with BLAST+Votes: 0GitHub stars: 4
- Bio Core Chromatogram AnalysisSanger sequencing chromatogram analysis — reading .ab1 files with BioPython, Phred quality scores, trace visualization, and quality-based trimmingVotes: 0GitHub stars: 4
- Bio Core Comparative GenomicsDot plots, synteny analysis, genomic rearrangement detection, ortholog/paralog distinction, pan-genome concepts, and tool selection for pairwise genome alignment.Votes: 0GitHub stars: 4
- Bio Core Computational Genetics- Build the standard genetic code programmatically and translate DNA to protein - Understand codon degeneracy and compute codon usage statistics (RSCU, CAI) - Perform virtual restriction enzyme digestVotes: 0GitHub stars: 4
- Bio Core DomainsSequence motifs and protein domains — PWM construction, PWM scanning, information content, sequence logos, PROSITE patterns, and Pfam/HMMER conceptsVotes: 0GitHub stars: 4
- Bio Core Gene OntologyGene Ontology structure, evidence codes, enrichment analysis with hypergeometric test and BH correctionVotes: 0GitHub stars: 4
- Bio Core Hic AnalysisHi-C Analysis: 3D Genome Organization with MatplotlibVotes: 0GitHub stars: 4
- Bio Core Motif DiscoveryPWM construction, scoring, threshold selection, and motif scanning for transcription factor binding sitesVotes: 0GitHub stars: 4
- Bio Core Multiple Sequence AlignmentProgressive MSA algorithms, tool selection by dataset size, guide tree construction, and profile alignmentVotes: 0GitHub stars: 4
- Bio Core Nucleic Acid StructureDNA helix forms (A/B/Z), groove geometry, nearest-neighbor thermodynamics, RNA secondary structure elements and dot-bracket notationVotes: 0GitHub stars: 4
- Bio Core Pairwise Sequence AlignmentPairwise Sequence Alignment with NumPyVotes: 0GitHub stars: 4
- Bio Core PathwaysGene Ontology and pathway enrichment — GO structure, hypergeometric/Fisher test, ORA vs GSEA, Benjamini-Hochberg FDR, KEGG/Reactome API patterns.Votes: 0GitHub stars: 4
- Bio Core PhylogeneticsPhylogenetics with BioPython: distance models (p-distance, JC69, K2P), UPGMA vs NJ tree construction, Newick parsing, and bootstrap interpretation.Votes: 0GitHub stars: 4
- Bio Core Protein StructureProtein structure analysis with BioPython Bio.PDB — SMCRA hierarchy, distance/RMSD calculations, DSSP secondary structure assignment.Votes: 0GitHub stars: 4
- Bio Core Sequence MotifsPWM/PFM/PPM construction, scoring, scanning, information content, sequence logos, and PROSITE pattern conversion.Votes: 0GitHub stars: 4
- Bioinformatics Workflows CicdSnakemake, Nextflow DSL2, GitHub Actions CI, and pytest patterns for bioinformatics pipelines.Votes: 0GitHub stars: 4
- Biopython DatabasesBioPython Seq/SeqRecord/SeqIO, NCBI Entrez API, UniProt queries, and biological format conversionVotes: 0GitHub stars: 4
- Cheminformatics Drug DiscoveryCheminformatics and drug discovery — RDKit molecular representations, fingerprints, Tanimoto similarity, QSAR modeling with ChEMBL data, AutoDock Vina docking, ADMET prediction, graph neural networks for moleculesVotes: 0GitHub stars: 4
- Chipseq EpigenomicsChIP-seq processing pipeline, peak calling with MACS3, differential binding with DiffBind, peak annotation with ChIPseeker, deepTools visualizationVotes: 0GitHub stars: 4
- Clinical Modeling WorkflowsACMG/AMP variant classification, in silico predictors, AutoDock Vina docking, GROMACS MD setup, and Scanpy single-cell analysis.Votes: 0GitHub stars: 4
- Dna MethylationBisulfite sequencing analysis: WGBS/RRBS processing, DMR calling, and epigenetic clock estimation.Votes: 0GitHub stars: 4
- Document RagRetrieval-augmented generation pipelines for document understanding.Votes: 0GitHub stars: 4
- Foundations Bash ScriptingBash scripting essentials for bioinformatics: variables, conditionals, loops, and pipeline patterns.Votes: 0GitHub stars: 4
- Foundations Biostatistics FundamentalsBiostatistics fundamentals: descriptive statistics, distributions, hypothesis testing, and confidence intervals for biological data. Use when analyzing experimental results.Votes: 0GitHub stars: 4
- Foundations Character EncodingsEvery bioinformatics pipeline starts with reading data from files. FASTA sequences, GenBank records, PDB coordinates, GFF annotations -- they all live as bytes on disk. When your Python script reads gVotes: 0GitHub stars: 4
- Foundations Git Version ControlGit for bioinformatics — setup, staging workflow, .gitignore, history navigation, undo operations, and branches.Votes: 0GitHub stars: 4
- Foundations Linux FundamentalsLinux command-line essentials for bioinformatics: navigation, file ops, pipes, grep, file format inspection, and vim survival guide.Votes: 0GitHub stars: 4