Pavel-Kravchenko/Bioinformatics - 第 5 页

generative-imaging

Restore images (denoising, inpainting, super-resolution) via DDRM SVD data-consistency projection with DDIM diffusion sampling in NumPy. Use for cryo-EM/MRI restoration or inverse problems y=Hx with a diffusion prior.

原文语言：英语

genomic-foundation-models

Choose/run DNA foundation models (Nucleotide Transformer, HyenaDNA, Evo, Enformer, Borzoi) via transformers: embed sequences, fine-tune, score variants with Enformer ISM. Use for genomic LLM choice or variant scoring.

原文语言：英语

genomic-llm-embeddings

Build DNA embeddings via k-mer frequency vectors or genomic LMs (Nucleotide Transformer, DNABERT-2, HyenaDNA). Use when embedding DNA for ML, choosing k-mer/BPE tokenization, or probing embedding quality.

原文语言：英语

genomics-to-structure-triage

Route coding variants to AlphaFold2/3 or RoseTTAFold and rank by missense/expression/rarity evidence weighted by pLDDT/PAE confidence. Use when triaging variants for structure prediction or picking AlphaFold vs RoseTTAFold.

原文语言：英语

graphs-dynamic-programming

Implement BFS/DFS, Dijkstra, Kruskal/Prim MST, topological sort, and DP (knapsack, Needleman-Wunsch, Smith-Waterman) in Python. Use for from-scratch alignment, PPI shortest paths, phylogenetic MST, gene-panel knapsack selection.

原文语言：英语

immunogenomics

Analyze scTCR/BCR-seq with scirpy on 10x VDJ contigs, type HLA with OptiType, and score neoantigens with NetMHCpan/pVACseq. Use when doing clonotype/repertoire analysis, HLA typing, or building neoantigen pipelines.

原文语言：英语

linear-tree-hash-structures

Implement Python linked lists, stacks/queues, BST/AVL/Red-Black trees, hash tables, Bloom filters with Big-O tradeoffs. Use when choosing a data structure, k-mer hash counting, VCF dedup Bloom filters, or interval trees.

原文语言：英语

linux-git-bash

Write set -euo pipefail bash pipelines, parse FASTA/FASTQ/VCF/GTF/BED with grep/awk/sed and BAM with samtools, and run git workflows. Use when writing/debugging shell scripts or fixing git/BOM/CRLF issues.

原文语言：英语

long-read-sequencing

Basecall ONT POD5 with Dorado, align with Minimap2, assemble with Flye/Hifiasm, call SVs with Sniffles2. Use when basecalling nanopore reads, doing long-read assembly, SV calling, or ONT methylation/isoform analysis.

原文语言：英语

metabolomics

Parse LC-MS mzML with pyOpenMS, PQN/LOESS-normalize feature tables, match m/z to HMDB/GNPS by ppm, run COBRApy FBA. Use when doing metabolomics preprocessing, metabolite ID, feature QC, MSEA enrichment, or flux modeling.

原文语言：英语

metagenomics-amplicon

Compute 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.

原文语言：英语

metagenomics-shotgun

Run 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.

原文语言：英语

network-biology

Build PPI networks from STRING with NetworkX, find hub genes via centrality, detect Louvain modules, infer GRNs with GENIE3. Use for protein interaction networks, hub/bottleneck genes, network communities, GRN inference.

原文语言：英语

population-structure-qc

Detect and correct for population stratification and cryptic relatedness in genotype data using PCA, kinship/IBD estimation, and genomic inflation factor (lambda) diagnostics before running a GWAS. Use when doing ancestry PCA, checking sample relatedness,…

原文语言：英语

protein-language-models

Embed proteins with ESM2, predict structure via ESMFold, zero-shot score mutations with ESM-1v, or design sequences via ESM-IF1 (fair-esm). Use for protein embeddings, MSA-free structure, DMS/VUS scoring, fixed-backbone design.

原文语言：英语

python-advanced-sql

Write Python decorators/context managers/dataclasses and query gene/variant tables with sqlite3/pandas SQL (JOIN, GROUP BY, HAVING). Use for retry/caching/validation wrappers or SQL against Ensembl/UCSC-style schemas.

原文语言：英语

python-bio-classes

Build Python classes for Gene/DNA/RNA/Protein records with __eq__/__lt__/__hash__, @property validation, ABCs, and @classmethod parsers (from_fasta_string). Use when modeling genes/FASTA/GFF as objects or asked about Python OOP, inheritance, dataclasses.

原文语言：英语

python-bio-comprehensions

Write Python comprehensions/generator expressions to filter, transform, count DNA/RNA/protein sequences (GC%, codons, k-mers, ORFs). Use when refactoring loop-heavy sequence code or streaming FASTA/FASTQ memory-efficiently.

原文语言：英语

python-bio-context-managers

Build Python context managers (__enter__/__exit__, @contextmanager, sqlite3) for safe FASTA I/O, temp cleanup, DB transactions. Use for leaked file handles, temp files surviving crashes, or with-compatible readers/writers.

原文语言：英语

python-bio-control-flow

Write if/elif/for/while loops over DNA/RNA/protein strings: codon iteration, stop-codon/motif scanning, GC-content classification. Use when looping over sequences, extracting codons, or debugging an off-by-one loop.

原文语言：英语

python-bio-data-types

Use Python's int, float, str, bool, and None types to represent and validate biological data (sequence lengths, GC content, DNA/RNA strings, missing annotations) and convert between them when parsing text records. Use when writing beginner Python for…

原文语言：英语

python-bio-data-visualization

Build volcano/MA plots, clustermap heatmaps, and multi-panel GridSpec figures with matplotlib/seaborn. Use when plotting DE results, expression data, or QC distributions, or fixing savefig, log-axis, colormap bugs.

原文语言：英语

python-bio-data-wrangling

Clean/reshape bio pandas tables — impute NaNs, dedupe replicates, coerce clinical strings to numeric/categorical, melt/pivot wide-long, regex-parse GTF attrs. Use for cleaning expr/clinical dataframes or reshaping.

原文语言：英语

python-bio-decorators

Write @decorators (functools.wraps, @lru_cache, factories) to time, validate, and memoize bio functions. Use for pipeline timing/logging, DNA/protein alphabet checks, caching codon/alignment calls, or decorator stacking.

原文语言：英语

python-bio-dictionaries

Use Python dict/defaultdict/Counter/set to translate codons, count k-mers, group genes by chromosome, and compare gene lists (union/intersection). Use when translating DNA, counting k-mers, or comparing gene sets.

原文语言：英语

python-bio-error-handling

Handle malformed FASTA/GFF via try/except/else/finally, custom exceptions, raise-from chaining. Use for parsers crashing on bad input, strict vs lenient FASTA parsing, KeyError/IndexError/ValueError, or batches skipping bad records.

原文语言：英语

python-bio-expressions

Use Python arithmetic and comparison operators to compute GC content, codon/frame math, protein MW, and primer Tm. Use when calculating GC%, codon counts, reading frames, or fixing operator-precedence bugs in bio scripts.

原文语言：英语

python-bio-file-operations

Read/write FASTA, FASTQ, CSV/TSV (BED), JSON, and pickle files in Python using open()/context managers, csv.DictReader/DictWriter, and streaming generators for large genomics files. Use when parsing a FASTA/FASTQ file, writing sequences back out with line…

原文语言：英语

python-bio-functions

Write 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.

原文语言：英语

python-bio-generators

Write Python generators (yield, itertools) for streaming FASTA/FASTQ readers, sliding-window GC/k-mer scans, and lazy translation pipelines that skip loading whole files into memory. Use for large FASTA/FASTQ parsing or MemoryError on genomic data.

原文语言：英语

python-bio-iterators

Stream 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.

原文语言：英语

python-bio-lists

Split CDS into codons, extract k-mers, sort sequences by GC%/length, and pack gene coordinates into tuples/namedtuples. Use when looping over genes/codons/SNPs/BED intervals, computing sliding-window GC%, or detecting gene overlaps in Python.

原文语言：英语

python-bio-numpy

Vectorize bioinformatics math with NumPy — RPKM/CPM/TPM normalization, per-gene z-scores, broadcasting over genes x samples matrices, position weight matrices (PWM/PSSM) for motif scoring, and O(n) sliding-window GC content via cumsum. Use when normalizing…

原文语言：英语

python-bio-oop

Build Python classes with __getitem__/__contains__/__call__/__slots__ and mixins for sequence databases, sliceable sequences, motif scorers, low-memory variants. Use for custom bio classes or dunder/OOP/__slots__ code.

原文语言：英语

python-bio-operators

Apply //, %, 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.

原文语言：英语

python-bio-pandas

Manipulate bio DataFrames with pandas — loc/iloc selection, boolean/query filtering, groupby agg vs transform, left-join annotation merges, CSV/TSV expression-matrix I/O, wide/long melt. Use when indexing/filtering a gene or sample table, merging expression…

原文语言：英语

python-bio-python-introduction

Foundational Python for biology - count nucleotides, compute GC content, use f-strings/loops/functions, and set up biopython/pandas/numpy via pip/venv/conda. Use when a beginner asks how to start with Python for bioinformatics, write a first DNA-parsing…

原文语言：英语

python-bio-regular-expressions

Match DNA/RNA/protein patterns with Python re — ORFs, restriction sites, IUPAC primers, PROSITE motifs, FASTA headers. Use when finding start/stop codons, tandem repeats, or parsing headers/BLAST output with regex.

原文语言：英语

python-bio-sequences

Manipulate 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…

原文语言：英语

python-bio-sets

Python set ops (union/intersection/difference) and collections.Counter for gene-list comparisons and k-mer/codon counting. Use when comparing gene lists, finding shared orthologs, computing k-mer Jaccard similarity, or tallying GC/codon usage.

原文语言：英语