pavel-kravchenko
- 213 skills
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- 1 day ago last updated
- ▌ Metagenomics Shotgun · pavel-kravchenkoRun Bowtie2 decontamination, Kraken2/Bracken classification, HUMAnN3 pathways, and MEGAHIT/MetaBAT2/CheckM MAG recovery on shotgun metagenomes. Use for WMS/WGS metagenomics, microbiome profiling, or MAG binning.
- ▌ Python Bio Functions · pavel-kravchenkoWrite Python `def` functions for bio scripts — ORF finders, reverse-complement, Hamming distance, *args/**kwargs, @lru_cache. Use for a mutable-default-argument bug, *args/**kwargs signatures, or reusable sequence helpers.
- ▌ Python Bio Iterators · pavel-kravchenkoStream FASTA/FASTQ and generate k-mers/codons lazily with Python generators, custom __iter__/__next__ classes, and itertools. Use when parsing multi-GB sequence files without loading them fully into RAM or chaining filter-trim-translate pipelines.
- ▌ Python Bio Operators · pavel-kravchenkoApply //, %, and 'in' operators to DNA/protein data — codon math, reading frames, GC precedence, stop-codon lookups. Use when computing GC content, finding reading frames, filtering by QC, or fixing precedence bugs.
- ▌ Python Bio Sequences · pavel-kravchenkoManipulate DNA/RNA/protein sequences as raw Python strings: reverse complement via str.maketrans/translate, transcription, codon/ORF extraction, motif and restriction-site scanning with find()/re, and hand-rolled FASTA parsing without Biopython. Use when writing sequence utilities from scratch, debugging off-by-one slicing or 1-based-vs-0-based coordinate errors, or when Biopython/Seq is unavailable or overkill.
- ▌ Python Bio Variables · pavel-kravchenkoDeclare and manipulate Python variables and core data types (int, float, str, bool, None) for bioinformatics scripts — naming, mutability, references, string slicing/indexing of DNA/RNA/protein sequences. Use when writing beginner Python for biology, explaining variable assignment/reassignment, debugging aliasing or mutable-default-argument bugs, or parsing sequence strings and FASTA headers with slicing/split/join.
- ▌ AI Science Vision RAG · pavel-kravchenkoColPali-style Vision RAG: embed rendered PDF pages, retrieve via ColBERT MaxSim, feed top-k pages to Qwen2-VL, no OCR. Use for PDF/document QA over figures and tables, multimodal retrieval, or Recall@k/MRR eval.
- ▌ Algo Basic Algorithms · pavel-kravchenkoCompute GCD/LCM via Euclid's algorithm, find roots with Newton's method, and count k-mers using dict/Counter vs O(n^2) list-scan. Use for GCD/LCM math, root-finding, k-mer counting, or Big-O complexity questions.
- ▌ Algo Comparison Sorts · pavel-kravchenkoImplement bubble/merge/shell/quicksort in Python; compare Big-O time/space/stability. Use when asked to sort an array, code a sort from scratch, explain quicksort complexity, or fix O(n^2) worst case on sorted input.
- ▌ Algo Mst Kruskal Prim · pavel-kravchenkoCompute minimum spanning trees with Kruskal's (Union-Find) and Prim's (min-heap) algorithms in Python or networkx. Use when building a phylogenetic distance tree, gene co-expression network backbone, MST-based clustering, or implementing Union-Find/disjoint-set.
- ▌ Algo Topological Sort · pavel-kravchenkoOrder vertices of a directed acyclic graph (DAG) with DFS-based or Kahn's BFS-based topological sort, detect cycles, and compute critical-path/makespan for weighted task DAGs. Use when scheduling a gene regulatory cascade, metabolic pathway, or bioinformatics pipeline (FastQC->Trimmomatic->STAR->featureCounts->DESeq2), resolving build/task dependency order, or checking whether a directed graph is acyclic.
- ▌ Bio Core Hic Analysis · pavel-kravchenkoAnalyze 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, TADs, A/B compartments, or .cool/.mcool contact matrices.
- ▌ Metagenomics Amplicon · pavel-kravchenkoCompute 16S/ITS amplicon diversity (Shannon, Simpson, Bray-Curtis, UniFrac), PCoA/NMDS ordination, PERMANOVA on OTU/ASV tables from QIIME2/DADA2. Use for 16S microbiome analysis.