gtars
Category: life-sciences · License: MIT · Version: 1.3 · Includes scripts
Tags: genomic intervals, BED files, peak sets, genomics, bioinformatics
When to use it
Inspects and plans work with Gtars, the Rust/Python/CLI toolkit for genomic intervals: BED RegionSet set algebra (reduce, setdiff, intersect, closest, cluster, gaps), overlap counts, consensus peak sets, coverage, tokenizers, fragment processing, and refget/BEDbase stores. Use when merging or comparing BED interval sets, building a consensus or universe from peaks, tokenizing regions for ML models, working with fragment files, or planning refget sequence-collection and BEDbase cache use. Use when checking BED coordinates, contigs, or strand before running gtars. Not for general BAM/VCF processing; use samtools or bedtools for that.Example requests
Ask your agent in plain language, for example:- “How do I get the union of two peak BED files into one non-overlapping set with gtars?”
- “I have 24 ATAC-seq replicate peak files (hg38, narrowPeak trimmed to BED) in ./peaks/ from 8 donors. I want a consensus peak set to use as the universe for tokenizing cells for a scEmbed-style model, and then train/val/test splits. I tried
from gtars import RegionSetand got an ImportError. Can you plan this out?” - “I have a few thousand enhancer regions and a set of GWAS hit windows. I want to know which enhancers sit nearest each hit, plus the stretches of genome not covered by either list. Some of my files use ‘1’ and others use ‘chr1’ for contigs. What’s the safest way to go about it?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.