How ritikadawadi/g-quadruplex-snp-research works
This repository is a reproducible genomics analysis project studying whether germline ClinVar SNVs in G-rich sequence alter predicted G-quadruplex stability in cancer-gene regulatory regions. Its principal workflow selects transcripts and extracts TSS, 5′UTR, and 3′UTR sequences; predicts reference motifs; identifies overlapping variants; constructs mutant sequences; predicts mutant motifs; and compares the results. Separate analysis scripts produce comparison, clinical, COSMIC-context, positional, and poster outputs. The pipeline links below follow the README; sampled excerpts show implementation details for several stages, but unsampled scripts are represented only at their documented subsystem level.
Main entry points: compare_mutant_wild Comparison Tables · results_compare_figures Analysis Results · run_qgrs_on_multifasta.py QGRS Runner · select_transcripts_and_extract_regions.py Transcript Extraction
Components 26
Genes & Regions
- Cancer Gene List
gene/oncogens.tsv - Genome & Annotation
data/reference - Transcript Extraction
scripts/select_transcripts_and_extract_regions.py - Region Coordinates
data/regions - Reference Sequences
data/fasta
Variant Analysis
- ClinVar Variants
data/clinvar - UTR Variant Discovery
scripts/find_spliced_qgrs_clinvar_snps.py - TSS Variant Discovery
scripts/find_tss_qgrs_clinvar_snps.py - QGRS Variant Overlaps
initial_snp - Mutant Sequence Builder
scripts/create_mutant_fasta_from_g_related_snps.py - Mutant Sequences
mutant_fasta
QGRS Comparison
- Reference QGRS
initial_fasta - QGRS Runner
scripts/run_qgrs_on_multifasta.py - qgrs-cpp
qgrs-cpp - Mutant QGRS
mutant_qgrs - Wild-Mutant Comparison
scripts/compare_qgrs_wild_vs_mutant.py - Comparison Tables
compare_mutant_wild
Reporting & Interpretation
- Comparison Figures
scripts/make_compare_figures.py - Clinical Impact
scripts/make_bio_clinical_gscore_impact_figures.py - COSMIC Context
scripts/make_cosmic_context_figures.py - Distinct Change Reports
scripts/write_distinct_change_reports.py - Positional G-score
scripts/make_positional_gscore_heatmap.py - Poster Core Figures
scripts/make_final_poster_core_figures.py - Top-Gene Tables
scripts/make_top_gene_clinvar_table_figures.py - Analysis Results
results_compare_figures
Other components
- Researcher
Connections 39
- Researcher → Transcript Extraction: starts analysis
README.md - Cancer Gene List → Transcript Extraction: selects genes
README.md - Genome & Annotation → Transcript Extraction: provides annotation
README.md - Transcript Extraction → Region Coordinates: writes coordinates
README.md - Transcript Extraction → Reference Sequences: extracts sequences
README.md - Reference Sequences → QGRS Runner: provides sequences
README.md - QGRS Runner → qgrs-cpp: runs prediction
README.md - QGRS Runner → Reference QGRS: writes reference hits
README.md - Reference QGRS → UTR Variant Discovery: provides motifs
README.md - Reference QGRS → TSS Variant Discovery: provides motifs
README.md - Region Coordinates → UTR Variant Discovery: provides regions
README.md - Region Coordinates → TSS Variant Discovery: provides regions
README.md - ClinVar Variants → UTR Variant Discovery: provides variants
README.md - ClinVar Variants → TSS Variant Discovery: provides variants
README.md - UTR Variant Discovery → QGRS Variant Overlaps: writes overlaps
README.md - TSS Variant Discovery → QGRS Variant Overlaps: writes overlaps
README.md - QGRS Variant Overlaps → Mutant Sequence Builder: selects G-related SNVs
README.md - Reference Sequences → Mutant Sequence Builder: provides reference sequence
README.md - Mutant Sequence Builder → Mutant Sequences: writes mutants
README.md - Mutant Sequences → QGRS Runner: provides sequences
README.md - QGRS Runner → Mutant QGRS: writes mutant hits
README.md - Reference QGRS → Wild-Mutant Comparison: provides reference results
README.md - Mutant QGRS → Wild-Mutant Comparison: provides mutant results
README.md - Mutant Sequences → Wild-Mutant Comparison: provides manifest
README.md - Wild-Mutant Comparison → Comparison Tables: writes deltas
README.md - Comparison Tables → Comparison Figures: summarizes changes
README.md - Comparison Tables → Clinical Impact: analyzes significance
README.md - Comparison Tables → COSMIC Context: joins cancer context
README.md - Comparison Tables → Distinct Change Reports: reports distinct changes
README.md - Comparison Tables → Positional G-score: maps positional effects
README.md - Comparison Tables → Poster Core Figures: summarizes results
README.md - Comparison Tables → Top-Gene Tables: ranks genes
README.md - Comparison Figures → Analysis Results: writes figures
README.md - Clinical Impact → Analysis Results: writes figures
README.md - COSMIC Context → Analysis Results: writes figures
README.md - Distinct Change Reports → Analysis Results: writes reports
README.md - Positional G-score → Analysis Results: writes figures
README.md - Poster Core Figures → Analysis Results: writes figures
README.md - Top-Gene Tables → Analysis Results: writes tables
README.md