Bioinformatics utilities

Normalizes a bulk RNA-seq count matrix using CPM and log2(CPM + 1). Intended as a compute-friendly building block for downstream analyses.

Lightweight heuristic checks for CRISPR guide RNAs: basic sequence validation, GC content, homopolymer flags, and optional PAM pattern matching.

Analyzes FASTQ quality metrics: per-base quality, GC content, and pass/fail summary.

Normalizes gene symbols to HGNC-approved symbols using MyGene.info. Returns a mapping table for ambiguous or outdated symbols.

Extracts structured, pipeline-friendly metadata from GEO accessions (e.g. GSE series, GSM samples) and returns a normalized summary.

Computes overlap between a user gene set and pathway gene sets using simple set metrics (intersection size and Jaccard index).

Suggests likely cell types from a list of top expressed genes using a small curated marker dictionary and simple overlap scoring.

Normalizes VCF text: sorts header lines, orders INFO fields, and validates basic structure.