bio-ribo-seq-translation-efficiency

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-ribo-seq-translation-efficiency --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: DESeq2 1.42+, 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 - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Translation Efficiency **"Calculate translation efficiency from my Ribo-seq and RNA-seq"** → Compute the ratio of ribosome occupancy to mRNA abundance per gene to identify translational regulation independent of transcription changes. - R: `riborex` for differential TE with DESeq2 backend - Python: Ribo-seq/RNA-seq count ratio with statistical testing ## Concept Translation Efficiency (TE) = Ribo-seq reads / RNA-seq reads - TE > 1: Efficiently translated (more ribosomes per mRNA) - TE < 1: Poorly translated - Changes in TE indicate translational regulation ## Calculate TE with Plastid ```python from plastid import BAMGenomeArray, GTF2_TranscriptAssembler import pandas as pd import numpy as np def ca