Version Compatibility

Reference examples tested with: numpy 1.26+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

miRge3 Analysis

"Quantify miRNAs with isomiR detection" → Fast miRNA annotation and quantification with isomiR variant detection and A-to-I RNA editing analysis from small RNA-seq reads.

• CLI: miRge3.0 annotate -s sample.fastq -lib human -db mirgenedb -o results/

Basic Quantification

Goal: Quantify known miRNA expression from small RNA-seq FASTQ files.