Pavel-Kravchenko/Bioinformatics - 第 6 页

python-bio-sql-for-bioinformatics

Query genomic data with SQLite (sqlite3, pandas.read_sql_query): SELECT/WHERE/GROUP BY/HAVING, INNER/LEFT JOIN, subqueries, parameterized inserts. Use when writing SQL over gene/variant tables or building a SQLite database.

原文语言：英语

python-bio-strings

DNA/RNA as Python strings: reverse complement (maketrans/translate), GC content, codon split, motif find (find/re.finditer), FASTA header parsing. Use for reverse complement, transcription, motif counting without Biopython.

原文语言：英语

python-bio-tuples

Build immutable Python tuple/namedtuple records for gene coordinates and SNP tuples (chrom,pos,ref,alt). Use when storing fixed records, returning multiple values, using coords as dict keys, or fixing list-aliasing/mutable-default bugs.

原文语言：英语

python-bio-variables

Declare 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,…

原文语言：英语

python-collections-regex

Python Counter/defaultdict/set for k-mer counting, streaming FASTA/FASTQ parsers, and re for restriction sites, codon motifs, PROSITE patterns. Use when extracting k-mers, streaming large sequence files, or regex-matching motifs/headers.

原文语言：英语

python-core-bio

Write pure-Python DNA/RNA sequence code (reverse complement, GC%, translation, ORF finding) and parse FASTA/FASTQ with generators. Use when writing sequence utilities without Biopython or parsing bio files from scratch.

原文语言：英语

rnaseq-analysis

Run bulk RNA-seq differential expression from a gene x sample count matrix using DESeq2 (R), pydeseq2, or edgeR — normalization (median-of-ratios/TPM), Wald/LRT testing, BH-adjusted p-values, volcano/MA plots, and GSEA/ORA. Use when doing RNA-seq DE,…

原文语言：英语

rnaseq

Run bulk RNA-seq DE with DESeq2/PyDESeq2: size-factor normalization, Wald test, apeglm LFC shrinkage, volcano/MA plots. Use for RNA-seq differential expression, TPM/FPKM/CPM, or STAR/Salmon/featureCounts to DESeq2 pipelines.

原文语言：英语

scrna-seq-analysis

Process 10x/Smart-seq scRNA-seq count matrices in scanpy/AnnData end-to-end — QC filtering, normalization, HVG selection, PCA/UMAP, Leiden clustering, marker genes, CellTypist annotation, and scVelo trajectory. Use when analyzing single-cell RNA-seq data,…

原文语言：英语

string-algorithms

Implement naive search, KMP (prefix function), Rabin-Karp (rolling hash), and DFA-based pattern matching in pure Python for exact substring/motif search in DNA or text. Use when finding restriction sites, scanning FASTQ/genome strings for a fixed motif,…

原文语言：英语

structural-bioinformatics

Parse PDB structures with Bio.PDB; compute RMSD/TM-score via Kabsch superposition; run DSSP/Ramachandran and PWM/PROSITE scans; GO/KEGG enrichment. Use when parsing PDB files, computing RMSD, or enriching genes via GO/KEGG.

原文语言：英语

virology-bioinformatics

Assemble viral genomes with iVar/minimap2, call intra-host SNVs with LoFreq, assign Nextclade/pangolin lineages. Use when trimming ARTIC primers, building a consensus FASTA, calling minority variants, or assigning a Pango lineage.

原文语言：英语

vision-language-models

Run VLM inference (Qwen2-VL, LLaVA, CLIP) via Transformers: captioning, VQA, zero-shot classification, chart data extraction. Use when captioning images, answering visual questions, or classifying images with no labels.

原文语言：英语