Results for “genomics”

Read, write, and analyze genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.

Read, write, and manipulate genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.

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.

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.

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.

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.

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.

Look up NHS England genomic tests for rare and inherited diseases. Use this skill whenever a clinician asks what genetic test to order for a condition, which genes are covered for a specific diagnosis, what commissioning category a genomic test falls under (Core, Specialised, or Highly Specialised), or which tests belong to a specialty group (Neurology, Cardiology, Endocrinology, etc.). Also trigger for questions like what panel is used for a condition, whether there is an NHS test for something, what the R number is for a condition, or whether anything has changed in the genomic test directory. Source: NHS England National Genomic Test Directory for Rare and Inherited Disease v9.0 (April 2026).

Runs high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the performance-critical backend for the geniml ML library. Use when computing overlaps/jaccard/coverage between BED region sets, indexing intervals with IGD, generating uniwig accumulation/coverage tracks, tokenizing genomic regions for ML, splitting single-cell fragments into pseudobulks, or computing GA4GH refget sequence digests. NOT for training region embeddings (use alterlab-geniml) or non-genomic spatial joins (use alterlab-geopandas). Part of the AlterLab Academic Skills suite.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Use when you need to index or query tab-delimited genomic files for fast region-based retrieval.

Toolkit de alta performance para análise de intervalos genômicos em Rust com bindings Python. Use ao trabalhar com regiões genômicas, arquivos BED, tracks de cobertura, detecção de sobreposições, tokenização para modelos de ML, ou análise de fragmentos em genômica computacional e aplicações de aprendizado de máquina.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Atomic-design guidance for Organisms — complex feature-level sections (Header, ProductGrid, CommentSection) that compose molecules, connect to state, handle loading/error/empty states, and own responsive layout decisions. Use when authoring components under ui/organisms or deciding molecule vs organism boundaries.

Analyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.

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.

Retrieve deterministic search results, metadata, and full-document Markdown from arXiv, PubMed/PMC, and US policy corpora with daily freshness checks.

Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs), searching by TF name, species, or class, scanning DNA sequences for binding sites, and comparing matrices. Use when doing motif analysis, regulatory genomics, transcription factor binding prediction, or interpreting regulatory/non-coding GWAS variants. Part of the AlterLab Academic Skills suite.