Results for “genome-completeness”

Automates genome-wide association studies from genotype files to publication-ready results, running PLINK2 QC and REGENIE regression with Manhattan and QQ plots.

Improves multi-step research reliability with structured protocols for source validation, error recovery, and transparent reasoning.

Scores genetic compatibility between all male-female pairings in a Genomebook generation, ranking optimal mating pairs based on heterozygosity, trait complementarity, and disease risk.

Drive a planned change to 100% coverage across an entire codebase when a prior agent run stopped early. Use whenever a refactor, migration, rename, rule-application, or sweeping edit was planned and partially executed but left incomplete — i.e.

Analyzes raw genomic data (FASTQ/VCF) to generate non-medical wellness, longevity, and pharmacogenomic optimization protocols while keeping DNA processing local and private.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Perform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a non-coding/regulatory variant's effect on expression or chromatin, or doing in-silico mutagenesis of a locus. To LOOK UP a variant's population frequency prefer alterlab-gnomad; for its clinical significance prefer alterlab-clinvar; for protein-structure effects prefer alterlab-alphafold; for single-cell foundation models prefer alterlab-scgpt. Part of the AlterLab Academic Skills suite.

Translates raw genomic data into personalized health, longevity, and pharmacogenomic protocols for AI agents.

Perform fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames via the polars-bio library, serving as a scalable alternative to bioframe and bedtools.

Verifies that every number, comparison, and scope claim in a research paper matches raw result files, using a fresh cross-model reviewer with no prior context to prevent confirmation bias.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.