gtars
Analyze genomic intervals and coverage tracks
متاح أيضًا من: davila7
Process and analyze genomic interval data for bioinformatics research. Gtars provides high-performance tools for overlap detection, coverage analysis, and ML tokenization of genomic sequences.
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رفع في Claude
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اختبرها
استخدام "gtars". Find overlaps between my ChIP-seq peaks and gene promoters
النتيجة المتوقعة:
- Overlapping peaks: 1,234 regions found
- Peak distribution: 45% in promoter regions, 30% in enhancers, 25% intergenic
- Results saved to peaks_in_promoters.bed
استخدام "gtars". Generate coverage track from ATAC-seq data
النتيجة المتوقعة:
- Coverage track generated: atac_coverage.bw
- Resolution: 10bp
- Total bases covered: 2.1 billion
- Peak accessibility regions identified: 150,000
التدقيق الأمني
آمنAll 209 static findings are false positives. The static analyzer incorrectly flagged markdown documentation syntax as security risks. No malicious code present. This is a legitimate genomic analysis toolkit.
عوامل الخطر
⚙️ الأوامر الخارجية (3)
📁 الوصول إلى نظام الملفات (1)
درجة الجودة
ماذا يمكنك بناءه
Peak overlap analysis
Identify overlapping regulatory elements and annotate variants by comparing ChIP-seq peaks.
Coverage visualization
Generate coverage tracks from ATAC-seq or ChIP-seq data for genome browser visualization.
Genomic ML preprocessing
Convert genomic regions into discrete tokens for training transformer models on DNA sequences.
جرّب هذه الموجهات
Use gtars to build an IGD index from my peaks.bed file and query overlaps with promoters.bed.
Generate a BigWig coverage track from my ATAC-seq fragments using gtars uniwig with 10bp resolution.
Create a TreeTokenizer from my training_regions.bed and tokenize the genomic coordinates for ML model input.
Split my fragments.tsv by cell barcodes using gtars fragsplit and output to cluster-specific directories.
أفضل الممارسات
- Use memory-mapped mode (mmap=True) when processing large genomic files for better performance.
- Build IGD indexes once and reuse them for multiple overlap queries.
- Specify thread count explicitly for predictable resource usage in batch processing.
تجنب
- Do not process GB-scale files without enabling memory-mapped mode.
- Avoid running multiple gtars commands sequentially when parallel processing is available.
- Do not skip format validation when integrating with external pipelines.