All authors
Claude Skills by Pavel-Kravchenko
github.com/Pavel-Kravchenko213 skills0 installs219 views
- Foundations ProbabilityProbability for Bioinformatics with NumPyVotes: 0GitHub stars: 4
- Foundations R FundamentalsR quick-reference for bioinformatics — syntax differences from Python, vectors, data frames, Bioconductor patterns, and statistical distributionsVotes: 0GitHub stars: 4
- Foundations R Hypothesis Testing And NonparametricsR hypothesis testing and nonparametric methods: binomial test, sign test, Wilcoxon, Kruskal-Wallis, and power analysis. Use when choosing and applying statistical tests in R.Votes: 0GitHub stars: 4
- Foundations R Regression Correlation And DiagnosticsR regression, correlation, and diagnostics: confidence intervals, t-tests, normality testing, Pearson/Spearman/Kendall correlation, Fisher z-transform CI.Votes: 0GitHub stars: 4
- Foundations Statistics PythonStatistics with PythonVotes: 0GitHub stars: 4
- Generative ImagingGenerative imaging and inverse-problem restoration workflows.Votes: 0GitHub stars: 4
- Genomic Foundation ModelsDNA/RNA sequence foundation models: embeddings, fine-tuning, and regulatory prediction.Votes: 0GitHub stars: 4
- Genomic Llm EmbeddingsDNA tokenization strategies, k-mer baselines, and pretrained sequence embeddings for genomic ML.Votes: 0GitHub stars: 4
- Genomics To Structure TriageRoute prioritized genomic variants into AlphaFold2/3 or RoseTTAFold structural follow-up.Votes: 0GitHub stars: 4
- Graphs Dynamic ProgrammingGraph algorithms (BFS, DFS, Dijkstra, MST, topological sort) and dynamic programming (memoization, tabulation, knapsack, sequence alignment)Votes: 0GitHub stars: 4
- ImmunogenomicsV(D)J repertoire analysis, HLA typing, and neoantigen prediction pipelines.Votes: 0GitHub stars: 4
- Linear Tree Hash StructuresLinked lists, stacks, queues, dynamic arrays, BST/AVL/Red-Black trees, hash tables with collision resolution, and Bloom filtersVotes: 0GitHub stars: 4
- Linux Git BashLinux shell commands, git workflows, bash scripting, and file encoding handling for bioinformatics data processing.Votes: 0GitHub stars: 4
- Long Read SequencingOxford Nanopore and PacBio long-read sequencing — basecalling (Dorado), QC (NanoStat), alignment (Minimap2), assembly (Flye, Hifiasm), SV calling (Sniffles2), methylation, isoform analysisVotes: 0GitHub stars: 4
- MetabolomicsMetabolomics analysis workflow: LC-MS data processing, metabolite identification, statistical analysis, and pathway mapping. Use when conducting metabolomics experiments.Votes: 0GitHub stars: 4
- Metagenomics Amplicon16S/amplicon metagenomics diversity and community analysis.Votes: 0GitHub stars: 4
- Metagenomics ShotgunShotgun metagenomics — host decontamination, Kraken2 taxonomic profiling, Bracken abundance, HUMAnN3 functional annotation, MEGAHIT assembly, MetaBAT2 binning, CheckM, MAGs, QIIME2 16SVotes: 0GitHub stars: 4
- Network BiologyBiological network analysis — PPI networks from STRING, NetworkX graph metrics, Louvain community detection, GO enrichment per module, Cytoscape export, gene regulatory network inference with GENIE3Votes: 0GitHub stars: 4
- Population Structure QcPopulation structure correction and stratification-aware QC for association studies.Votes: 0GitHub stars: 4
- Protein Language ModelsESM2 embeddings, ESMFold structure prediction, zero-shot mutation scoring, and protein design.Votes: 0GitHub stars: 4
- Python Advanced SqlOOP for bioinformatics classes, decorators, context managers, error handling, and SQL queries for biological databases.Votes: 0GitHub stars: 4
- Python Bio ClassesPython classes for bioinformatics — designing Sequence, Gene, and ProteinRecord classes with encapsulation, dunder methods, inheritance, ABCs, and properties.Votes: 0GitHub stars: 4
- Python Bio ComprehensionsPython comprehensions and generators for bioinformatics — list/dict/set comprehensions, generator expressions for large sequence files, bio-specific patterns.Votes: 0GitHub stars: 4
- Python Bio Context ManagersContext managers for safe file, database, and resource handling in bioinformatics pipelines.Votes: 0GitHub stars: 4
- Python Bio Control FlowPython control flow patterns specific to bioinformatics — codon iteration, frame scanning, motif search, sequence classification.Votes: 0GitHub stars: 4
- Python Bio Data TypesPython data types for bioinformatics: int, float, str, bool, None, and type conversions with biological examples. Use when learning how Python represents biological data.Votes: 0GitHub stars: 4
- Python Bio Data VisualizationMatplotlib and seaborn for bioinformatics figures: volcano plots, heatmaps, MA plots, genome tracks. Critical gotchas for publication-quality figures.Votes: 0GitHub stars: 4
- Python Bio Data WranglingPandas patterns for bio data — missing values, duplicates, type conversion, wide/long reshaping, string parsing, apply/transform/pipe.Votes: 0GitHub stars: 4
- Python Bio DecoratorsPython decorator patterns for bioinformatics: timing, validation, memoization, and stacking.Votes: 0GitHub stars: 4
- Python Bio DictionariesDictionaries and sets for bioinformatics: codon tables, nucleotide frequency, defaultdict grouping, Counter k-mers, and set operations on gene lists.Votes: 0GitHub stars: 4
- Python Bio Error HandlingRobust error handling for bioinformatics pipelines — custom exception hierarchy, try/except/else/finally, exception chaining, strict FASTA parsing.Votes: 0GitHub stars: 4
- Python Bio ExpressionsPython arithmetic, comparison, logical, and membership operators with bioinformatics applications — codon frames, GC content, quality filters.Votes: 0GitHub stars: 4
- Python Bio File OperationsFASTA/FASTQ/CSV parsing recipes, streaming file I/O patterns, and format-specific pitfalls for bioinformatics data filesVotes: 0GitHub stars: 4
- Python Bio FunctionsBio-specific function patterns — ORF finding, sequence analysis, mutable default trap, and functional programming idioms for bioinformaticsVotes: 0GitHub stars: 4
- Python Bio GeneratorsGenerator patterns for streaming bioinformatics data — FASTA/FASTQ readers, sliding windows, translation pipelines, and memory-efficient sequence processingVotes: 0GitHub stars: 4
- Python Bio IteratorsCustom iterators for bioinformatics — codon iteration, k-mer generation, streaming FASTA/FASTQ, and lazy sequence processing patternsVotes: 0GitHub stars: 4
- Python Bio ListsList and tuple patterns for bioinformatics — codon splitting, gene coordinate records, named tuples, sorting by GC/length, and copy pitfallsVotes: 0GitHub stars: 4
- Python Bio NumpyNumPy for bioinformatics — vectorized operations, broadcasting for expression matrices, PWM construction, sliding-window GC with cumsum, and normalization recipesVotes: 0GitHub stars: 4
- Python Bio OopOOP patterns for bioinformatics — subscriptable sequence databases, sliceable BioSeq, callable motif scorers, __slots__ for millions of variants, and composable mixinsVotes: 0GitHub stars: 4
- Python Bio OperatorsOperator pitfalls and idioms for bioinformatics — floor division for codons, modulo for reading frames, GC content precedence, and membership testingVotes: 0GitHub stars: 4
- Python Bio PandasNumPy arrays and Pandas DataFrames for bioinformatics — vectorized ops, broadcasting, CPM/RPKM normalization, PWM scoring, loc/iloc, groupby, and annotation merges.Votes: 0GitHub stars: 4
- Python Bio Python IntroductionPython Introduction for BioinformaticsVotes: 0GitHub stars: 4
- Python Bio Regular ExpressionsRegular expressions for biological sequence pattern matching — ORF finding, motifs, restriction sites, FASTA headers, overlapping matchesVotes: 0GitHub stars: 4
- Python Bio SequencesPython string operations for biological sequences: reverse complement, codon extraction, motif scanning, FASTA parsing. Bio-specific patterns and pitfalls.Votes: 0GitHub stars: 4
- Python Bio SetsSets and Counter for bioinformatics: gene list operations (intersection/union/difference), k-mer deduplication, and unique element tracking. Bio-specific patterns only.Votes: 0GitHub stars: 4
- Python Bio Sql For BioinformaticsEnsembl, UCSC Genome Browser, NCBI, and dbSNP are all backed by relational databases. Even locally, SQLite is a practical way to store and query gene annotations, variant tables, and expression resultVotes: 0GitHub stars: 4
- Python Bio StringsPython string operations for bioinformatics: reverse complement, GC content, motif finding, FASTA parsing. Bio-specific patterns and pitfalls only.Votes: 0GitHub stars: 4
- Python Bio TuplesLists and tuples for bioinformatics: codon extraction, genomic coordinate records, named tuples, and copy semantics. Bio-specific patterns only.Votes: 0GitHub stars: 4
- Python Bio VariablesPython variables and data types for bioinformatics — naming, mutability, references, numeric and string typesVotes: 0GitHub stars: 4
- Python Collections RegexPython collections (namedtuple, defaultdict, Counter, set) and regex for bioinformatics — k-mer counting, FASTA/FASTQ streaming, restriction maps, PROSITE patterns.Votes: 0GitHub stars: 4