Results for “dna-sequence”

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.

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

Performs differential expression analysis on bulk RNA-seq or pseudo-bulk count matrices with QC, PCA, and contrast testing.

Predicts gene and transcript structure from a DNA sequence using the hosted Genomic Intelligence API, producing a report and JSON output.

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

Annotates single-cell RNA-seq data by scoring marker genes, transferring labels with CellTypist, or reasoning over marker lists with an LLM.

Analyze any text to extract a cognitive fingerprint across 12 dimensions, revealing reasoning patterns, decision styles, and thinking signatures.

Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mapping.

Detect promoter regions in DNA sequences by calling the Genomic Intelligence G0 transformer (GENA-LM BERT Large) hosted API. Returns per-window promoter probabilities and called regions as a report and JSON, from a single FASTA input.

RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.

Analyzes sample phenotype and SNP genotype data to identify the best-performing homozygous genotype at each locus, excluding heterozygous and missing calls, and writes results to a CSV file.

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.