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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

This projects as a reproducible workflow for generating peptide-to-kinase annotations for the KRSA and reKRSA kinome analysis systems. This project utilizes the PamChip annotation files for each PamChip article numbers and the Sequence-based kinome atlas developed by Johnson et al (2023) Yaron-Barir et al (2024) to identify likely upstream kinases based on the substrate sequences.

Key Resources

Architecture

The project has a simple R-based pipeline with the following structure:

├── raw/                           # Raw layout files from KRSA (Layout.txt)
├── data/
│   ├── input_sequence_data.csv.bz2    # Prepared peptide sequences
│   └── individual/                 # Downloaded kinase specificity data (per peptide/chip)
├── results/
│   ├── complete_kinase_specificity_map.csv.gz       # Kinase map filtered to the top 20 targets by score for each peptide
│   ├── complete_kinase_specificity_map_raw.csv.gz   # Raw kinase map including all results for each peptide on each chip
├── scripts/
│   └── utf8_converter.sh            # Utility batch UTF-8 conversion script
└── R/
    ├── prepare_sequences.R          # Extract the sequences from each layout file and format the to be queried from the API
    ├── download_specificity_data.R  # Download data from GraphQL API

Data Pipeline Workflow

The annotation pipeline follows these steps:

  1. Layout Processing: Read Layout.txt files from raw/ directory
  2. UTF-8 Conversion: Convert legacy files to UTF-8 using scripts/utf8_converter.sh
  3. Sequence Preparation: Run prepare_sequences.R to:
    • Add * markers to S, T, Y residues
    • Generate phosphorylation variants
    • Handle ambiguous amino acids (B/Z)
    • Create phosphoprimer/phosphosite encodings
    • Output: data/input_sequence_data.csv.bz2
  4. Data Download: Run download_specificity_data.R to:
    • Query GraphQL API for each prepared sequence
    • Download kinase specificity scores
    • Output: results/complete_kinase_specificity_map.csv.gz

Common Development Tasks

Running the Full Pipeline

# Step 1: UTF-8 conversion (if needed)
bash scripts/utf8_converter.sh

# Step 2: Prepare sequences
Rscript R/prepare_sequences.R

# Step 3: Download data from API
Rscript R/download_specificity_data.R

# Step 4: Generate metrics
Rscript R/create_specificity_metrics.R

Running Individual R Scripts

# Prepare sequences only
Rscript R/prepare_sequences.R

# Download data only (uses cached data when files already exist)
Rscript R/download_specificity_data.R

# Generate metrics
Rscript R/create_specificity_metrics.R

Running a Single Test Script

To run a specific analysis script:

Rscript [script_name].R

Key R Packages Used

  • tidyverse (includes: dplyr, tidyr, purrr, tibble, readr, stringr)
  • httr2 (for HTTP requests to GraphQL API)
  • glue (for string interpolation)
  • stringi (for string operations)
  • UpSetR (for intersection visualization)

Configuration

.Rprofile

The project uses renv for package management. The .Rprofile automatically sources renv/activate.R.

.gitignore

  • .Rproj.user/, .Rhistory, .RData, .Ruserdata
  • *.log
  • x-*.R (downloaded data from API)
  • .vscode/

Note: Data files are excluded:

  • data/*.bz2 and results/*.gz are tracked (compression makes them reasonable to version)
  • raw_backup/ is excluded

renv

The project uses renv for reproducible R environments. Run renv::init() or renv::restore() as needed.

File Formats

Input: Layout.txt (from raw directory)

PeptideID<TAB>Sequence<TAB>GeneName<TAB>...

Output: input_sequence_data.csv.bz2 columns

  • ID - Composite identifier (Old_ID + phosphosite + priming + disambiguation)
  • PeptideID - Original peptide identifier
  • source_sequence - Original peptide sequence
  • prepared_sequence - Modified sequence with phosphorylation markers
  • phosphosite - Phosphorylation site location (e.g., "Y4")
  • priming_status - Priming location encoding (e.g., "0b0", "0b1")
  • disambiguation - Amino acid disambiguation code (e.g., "O0xO")
  • ChipArticleID - KRSA article identifier

GraphQL API Response

The GraphQL query returns kinase data including:

  • processedSequence - Processed sequence
  • kinases array with: family, geneName, name, percentile, percentileRank, score, scoreRank, uniprotId, displayName

Chip Types

  • STK: Serine/Threonine kinase chip (targets S/T residues)
  • PTK: Protein Tyrosine kinase chip (targets Y residues)

gstack

Use the /browse skill (from gstack) for all web browsing tasks.

Never Use

  • Never use mcp__claude-in-chrome__* tools — always use /browse instead.

Available Skills

Use these skills for planning, design, testing, and development tasks:

  • /office-hours — Brainstorming, idea exploration, startup thinking
  • /plan-ceo-review — CEO/founder-mode strategic review, scope expansion
  • /plan-eng-review — Engineering review, architecture, data flow, edge cases
  • /plan-design-review — Design critique, visual audits, layout review
  • /design-consultation — Design system creation, brand guidelines
  • /review — Pre-landing PR review, code review
  • /ship — Ship workflow: merge, CI, deploy, verify
  • /browse — Headless browser for QA testing and site dogfooding
  • /qa — Systematic QA testing, test and fix bugs
  • /qa-only — QA report mode: test without fixing
  • /design-review — Visual QA, design polish, fix visual issues
  • /setup-browser-cookies — Import cookies for authenticated testing
  • /retro — Engineering retrospective, commit history analysis
  • /investigate — Systematic debugging with root cause analysis
  • /document-release — Update documentation post-ship
  • /codex — Code review, challenge mode, second opinion
  • /careful — Safety mode: destructive command warnings
  • /freeze — Restrict edits to specific directory
  • /guard — Full safety: warnings + directory-scoped edits
  • /unfreeze — Clear edit restrictions
  • /gstack-upgrade — Upgrade gstack to latest version

Example Usage

# To view a website:
/browse

# To test a feature on a live site:
/browse

# For authentication before testing:
/setup-browser-cookies