Results for “rna-velocity”

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differentiation dynamics from spliced/unspliced layers (velocyto/STARsolo output); for the general QC, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for .h5ad data-structure I/O and layer wrangling prefer alterlab-anndata instead. Part of the AlterLab Academic Skills suite.

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.

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.

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

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

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

Use when calculating thermodynamics of RNA-RNA interactions, including accessibility and binding energy predictions for RNA duplex formation.

Evaluates RAG pipelines using a filesystem-based benchmark with corpus/ and train.json, running evaluate_rag.py to tune retrieval and generation flags and interpret RAGAS metrics.

Configure fault tolerance, straggler detection, preemption, in-process restart, and re-run state machine for Megatron Bridge training jobs.

Scale alignment for RNA-protein cross-modal integration - BOTH modalities must be z-scored

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

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

Generate images with Google Nano Banana 2 (Gemini-family flash-tier text-to-image) on RunComfy — bundled with the model's documented prompting patterns so the skill gets sharper output than naive prompting against the same model. Documents Nano Banana 2's strengths (rapid iteration, in-image typography rendering, predictable framing, optional web-grounded context), the resolution-tier pricing, the safety-tolerance dial, and when to route to Nano Banana Pro / GPT Image 2 / Flux 2 / Seedream instead. Calls `runcomfy run google/nano-banana-2/text-to-image` through the local RunComfy CLI. Triggers on "nano banana", "nano-banana-2", "nano banana 2", "google image gen", "gemini image", or any explicit ask to generate with this model.

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

Run replication, robustness, and specification-sensitivity workflows for Stata projects. Use when a researcher wants to reproduce a result, rerun a pipeline, compare specifications, audit a do-file sequence, or check whether a claim is stable.

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.

Generate images with Google Nano Banana 2 (Gemini-family flash-tier text-to-image) on RunComfy — bundled with the model's documented prompting patterns so the skill gets sharper output than naive prompting against the same model. Documents Nano Banana 2's strengths (rapid iteration, in-image typography rendering, predictable framing, optional web-grounded context), the resolution-tier pricing, the safety-tolerance dial, and when to route to Nano Banana Pro / GPT Image 2 / Flux 2 / Seedream instead. Calls `runcomfy run google/nano-banana-2/text-to-image` through the local RunComfy CLI. Triggers on "nano banana", "nano-banana-2", "nano banana 2", "google image gen", "gemini image", or any explicit ask to generate with this model.

RNN+Transformer hybrid with O(n) inference. Linear time, infinite context, no KV cache. Train like GPT (parallel), infer like RNN (sequential). Linux Foundation AI project. Production at Windows, Office, NeMo. RWKV-7 (March 2025). Models up to 14B parameters.

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

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.

GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, and other RAPIDS libraries for dramatic speedups on numerical, data, ML, graph, and simulation workloads.

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

Production-grade multi-threaded Rust vanity address generator for Solana — 100K+ keys/sec using Rayon parallel iterators with solana-sdk, Base58 pattern matching, prefix/suffix support, security-hardened file output, and Criterion benchmarks.

Local RAG indexing with 97% storage reduction via anchor-based lazy recomputation. Graph-based selective embedding storage for memory-efficient semantic code search.

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.

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