Results for “dna-annotation”

Add visual callouts like rectangles, arrows, and labels to screenshots, diagrams, and images using PIL/Pillow, with support for animated GIF annotations.

Use when you need to annotate BAM alignments with a two-character tag based on overlaps with BED, GFF, or VCF annotation files, such as labeling reads by feature class or interval source.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Create, read, manipulate, and store annotated data matrices using the AnnData Python package, designed for single-cell genomics and general-purpose annotated data workflows.

Use when annotating VCF files with flanking sequence information (INFO/FS tag) or masking regions/variants in flanking sequences.

Use when filling ancestral alleles into the INFO column of VCF files using ancestral alignment data from 1000 Genomes or similar sources.

Query gnomAD (Genome Aggregation Database) for population allele frequencies and gene constraint scores (pLI, LOEUF) reflecting loss-of-function intolerance. Use when checking how common a variant is across populations, filtering rare-disease candidate variants, assessing variant pathogenicity, or identifying loss-of-function intolerant genes. Part of the AlterLab Academic Skills suite.

Enumerate DNS records, attempt zone transfers, brute-force subdomains, and map DNS infrastructure during authorized reconnaissance to identify attack surface, misconfigurations, and information disclosure in target domains.

Use when a GFF file needs bcftools/csq-compatible gene and transcript attributes before consequence annotation.

Query gnomAD for population allele frequencies, constraint metrics, and loss-of-function intolerance. Use when interpreting variants, filtering common alleles, or prioritizing genes in rare disease workflows.

Use when converting compatible BLAST annotation XML/ASN streams into a compact gene-markup-style table for downstream EDirect interval helpers.

Orchestrates a dimensional-analysis pipeline to annotate codebases with unit/dimension comments, discover dimensional vocabulary, and detect arithmetic bugs from unit mismatches or precision loss.

Use when performing nucleotide-nucleotide similarity searches to identify homologs, annotate sequences, or compare query sequences against nucleotide databases.

Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.

Use when aligning short reads to a reference genome or indexed sequence database. Suitable for mapping FASTQ/FASTA reads in paired-end or single-end mode to produce SAM output.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Esta habilidade deve ser usada ao trabalhar com matrizes de dados anotados em Python, particularmente para análise de genômica de célula única, gerenciamento de medições experimentais com metadados ou manipulação de datasets biológicos em larga escala. Use quando as tarefas envolvam objetos AnnData, arquivos h5ad, dados de RNA-seq de célula única ou integração com ferramentas scanpy/scverse.

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

Use to build PNAS's Data Availability Statement and deposition plan — mandatory deposition of data in an approved repository at submission, accession numbers/DOIs, public + archived code, and materials sharing. "Available on request" is not sufficient for primary data.

Use before sensitive, clinical, identifying, or raw interview data is placed in front of an AI tool, when transcripts or student materials need de-identification, or when a data-minimization gate must run before any analysis or drafting.

Annotate the outline with where to mention specific brand products. Designed-in at outline time so product callouts feel natural in the draft, not bolted on.

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.