Results for “dhdna”

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.

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

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.

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

Detect anomalies in DNP3 protocol communications used in SCADA systems by monitoring for unauthorized control commands, firmware update attempts, protocol violations, and deviations from baseline traffic patterns using deep packet inspection and machine learning approaches.

Compiles SOUL.md character profiles into synthetic diploid genomes by mapping trait scores to alleles at defined loci, producing .genome.json files.

Perform cheminformatics tasks including molecular I/O, descriptor calculation, fingerprinting, substructure search, and similarity analysis using the RDKit library.

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

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

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.

Provides guidance for using RDKit to read and write molecular structures, calculate descriptors, generate fingerprints, perform substructure searches, and handle chemical reactions.

Manage Amazon Aurora DSQL clusters, schemas, and migrations with MCP tools and CLI scripts, including multi-tenant patterns and IAM-based authentication.

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization, specialized fingerprint or descriptor algorithms, reaction enumeration, or conformer generation demand direct API control; for a high-level pandas-friendly wrapper over RDKit prefer alterlab-datamol, and for turning molecules into ML feature vectors prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.

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

Performs differential expression analysis on label-free quantitative (LFQ) proteomics data from MaxQuant and DIA-NN outputs, including preprocessing, imputation, statistical testing, and visualization.