geniml
Category: life-sciences · License: MIT · Version: 1.2 · Includes scripts
Tags: genomic intervals, BED files, machine learning, embeddings, genomics
When to use it
Plans and audits local genomic-interval machine learning workflows with Geniml (0.8.4) and Gtars: validates BED files against chromosome sizes and assembly contracts, plans Region2Vec, scEmbed, and BEDspace runs, checks model, tokenizer, and universe.bed compatibility, and assesses consensus universes (CC, CCF, ML, HMM, assess-universe). Bundled scripts only validate or plan; they do not train. Use when checking BED coordinates, contigs, or assembly before analysis. Use when planning Region2Vec or scEmbed training on tokenized Parquet data. Use when verifying that a checkpoint, config.yaml, and universe match. Use when building or assessing a consensus peak universe. Use when reviewing BEDbase or Hugging Face download risks. Not for general BED manipulation or peak calling; use bedtools or similar tools.Example requests
Ask your agent in plain language, for example:- “Can you check my peaks.bed against hg38.chrom.sizes before I run anything? Worried about chr naming.”
- “I exported tokenized ATAC regions to data/tokens.parquet (list column ‘tokens’) using universe.bed from our GRCh38 lab pipeline and want to train Region2Vec. Before I burn GPU time, I got ‘size mismatch for projection.weight’ when loading models/r2v/checkpoint.pt with a config.yaml from a colleague. Help me figure out what’s wrong and plan the run.”
- “We have peak calls from 40 ChIP-seq experiments across several labs and want one common set of regions to use as a shared vocabulary for embedding models, then measure how well it fits our data. What’s a safe 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.