Results for “dnase”

Build and deploy apps/applets on the DNAnexus cloud genomics platform, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.

Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.

Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.

Runs and manages DNAnexus jobs and workflows, including monitoring, parallel execution, and error handling.

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

Diagnose failed or unhealthy Dynamo deployments by collecting a read-only debug bundle, classifying failures, and providing step-by-step remediation guidance.

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

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

Manages NS1 DNS zones, records, filter chains, monitoring jobs, and traffic steering via the NS1 API, with a discovery-first workflow for inspection and troubleshooting.

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

Takes pre-computed differential expression results from DESeq2, edgeR, limma, or PyDESeq2 and produces a structured, publication-ready summary with ranked gene lists, biological themes, and key observations.

Access the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.

You are an expert in Knex.js, the flexible SQL query builder for Node.js that supports PostgreSQL, MySQL, SQLite, and MSSQL. You help developers write type-safe queries with a chainable API, manage database migrations and seeds, build complex joins and subqueries, and use transactions — providing direct SQL control without the overhead of a full ORM.

Runs DNS, email security, SSL, WHOIS, and network checks by calling the dnsrobot.net API, with no API key required.

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.

Analyze .NET malware by decompiling and debugging assemblies with dnSpy, deobfuscating with de4dot, and extracting C2 configurations and IOCs.

Predicts enhancer activity in DNA sequences using the hosted Genomic Intelligence G0 DeepSTARR model, returning per-window activity scores.

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

DALL-E: Zero-Shot Text-to-Image Generation

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

Autonomous design space exploration loop for computer architecture and EDA. Runs a program, analyzes results, tunes parameters, and iterates until objective is met or timeout. Use when user says "DSE", "design space exploration", "sweep parameters", "optimize", "find best config", or wants iterative parameter tuning.

Sets up DNS records, SSL/TLS certificates, subdomains, email authentication, and health-check failover routing for Route53, Cloudflare, or GCP Cloud DNS, with optional Terraform output.

Expert guidance for distributed training with DeepSpeed - ZeRO optimization stages, pipeline parallelism, FP16/BF16/FP8, 1-bit Adam, sparse attention

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

Provides expert guidance for distributed training with DeepSpeed, covering ZeRO optimization stages, pipeline parallelism, FP16/BF16/FP8, 1-bit Adam, and sparse attention.

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

Detects DNS-based data exfiltration, tunneling, and DGA communication by analyzing query logs with entropy analysis, volume anomalies, and subdomain length detection in SIEM platforms.

Expert guidance for distributed training with DeepSpeed - ZeRO optimization stages, pipeline parallelism, FP16/BF16/FP8, 1-bit Adam, sparse attention

D&D 5e toolkit for players and DMs. Roll dice, look up spells and monsters, generate characters, create encounters, and spawn NPCs. Uses the official D&D 5e SRD API.

Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis.

Provides quick reference documentation for Dnscheck concepts, best practices, and implementation patterns, covering intro, quickstart, debugging, performance, security, migration, and cheatsheet topics.

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

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

Comprehensive guide to nvae. Master the concepts, implementation, best practices, and real-world applications of nvae in professional environments.

Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis.