Results for “rna-velocity”

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

Use when predicting RNA secondary structures, calculating minimum free energy (MFE) folds, or computing partition functions and base pairing probabilities for RNA sequences.

Use when computing RNA specific heat profiles from sequence data to analyze melting behavior and thermal stability across temperature ranges.

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

Use when converting ViennaRNA-style sequence-plus-dot-bracket records on stdin into RNA connectivity-table output.

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

Pino - extremely fast and low overhead Node.js logger with JSON-native structured logging. 10x faster than Winston. Optimized for high-performance APIs and production environments. USE WHEN: user mentions "pino", "fast logging", "high performance logging", "fastify logging", asks about "fastest node.js logger", "JSON structured logging", "low overhead logging" DO NOT USE FOR: Winston logging - use `winston` instead, Python logging - use `python-logging` instead, Complex transport requirements - use `winston` instead

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 summarizing an RNA folding landscape by counting how many structures fall into each energy band, rather than enumerating individual folds one by one.

Use when searching DNA or RNA queries against nucleotide sequence databases with HMMER's nucleotide homology search engine.

ORCA v2.0 — Gen-2 Striker with momentum event quality confirmation. FIRST_JUMP detection enhanced with Tier 2 momentum events and TCS trader quality tags. Stalker permanently removed. DSL exit managed by plugin runtime via runtime.yaml.

Vitest - Modern TypeScript testing framework with Vite-native performance, ESM support, and TypeScript-first design

Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.

Diagnosing and fixing bimodal matching score distributions in MaxFuse

Use when evaluating the free energy (kcal/mol) of an RNA secondary structure, calculating co-folding energies for two RNA strands, or analyzing consensus structures from multiple sequence alignments.

Frangi vesselness 3D filter: Ra formula correction, scikit-image deprecations, GPU VRAM guard

MaxFuse parameter tuning for datasets with large protein:RNA cell ratios (>100:1)

SONA self-optimizing neural architecture with ReasoningBank trajectory learning, EWC++ anti-forgetting, and reinforcement learning feedback loops.

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

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

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.

LLaVA-NeXT: Improved Reasoning, OCR, and World Knowledge

Alert design and on-call practices — severity, runbooks, SLO burn-rate alerting, escalation. Use when designing alerts, writing runbooks, reducing alert fatigue, setting up escalation policies, implementing SLO-based alerting, or improving on-call processes.