Results for “dna-sequence”

Use when working from the local Evo 2 repository for DNA-sequence scoring, embeddings, generation, or phage-genome design experiments.

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Provides Python bindings to interact with the DNAnexus platform, enabling file uploads, job management, and API calls.

Use when profiling nucleotide content (AT/GC percentages, base counts) of genomic intervals against a FASTA reference.

Query 20+ bioinformatics databases from the command line or Python for gene information, sequences, protein structures, enrichment analysis, and more.

Análise de RNA-seq de célula única. Carregue dados .h5ad/10X, QC, normalização, PCA/UMAP/t-SNE, clustering Leiden, genes marcadores, anotação de tipo celular, trajetória, para análise de scRNA-seq.

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.

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.

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

Detects DNS tunneling by computing Shannon entropy of DNS query names, analyzing query length distributions, inspecting TXT record payloads, and identifying high subdomain cardinality using scapy for packet capture analysis.

Perform differential gene expression analysis for bulk RNA-seq data using PyDESeq2, supporting formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.

Process and analyze high-throughput sequencing data with deepTools for quality control, normalization, comparison, and publication-quality visualizations of ChIP-seq, RNA-seq, and ATAC-seq experiments.

Use when searching protein query sequences against a translated nucleotide database to identify protein-coding regions or homologs in genomic data.

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

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.

Generates and reviews MariaDB CREATE SEQUENCE statements with version-specific syntax, defaults, and gotchas.

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).

Use when aligning RNA-seq reads to a reference genome with junction detection, including exon-exon junctions and gene fusions.

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.