Results for “dna”

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

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.

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.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

DNS records, IP addressing, subnetting, common protocols, and diagnostic tools. Use when configuring DNS records, debugging resolution or connectivity, planning subnets, analyzing HTTPS/TLS errors, or diagnosing latency and routing issues.

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

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 the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

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.

Detects command-and-control (C2) communications tunneled through DNS protocol, including DNS tunneling tools, domain generation algorithms, and encoded payload delivery via TXT/CNAME records.

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

Use when converting RNA connectivity-table (`.ct`) files into extended FASTA with dot-bracket structures, optionally removing pseudoknots or modified bases.

Analyze Zeek dns.log files to detect DNS-based data exfiltration by computing Shannon entropy, flagging long subdomain labels, and identifying anomalous query patterns.

Use when simulating stochastic folding kinetics of single-stranded nucleic acids, computing first passage times between structures, or analyzing RNA/DNA folding trajectories.

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

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.