Results for “rna-synthesis”

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

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

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

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

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

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

Merge many sources into one cited, deduplicated answer with per-claim confidence.

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.

李娜（网球 / 体育）认知与表达框架（压缩蒸馏）：个性球员叙事、怼媒体金句、职业化独立 触发：法网、直率采访 等。非替本人编造

Use when filtering `RNAsubopt -s` output to keep p-optimal RNA structures in a ViennaRNA post-processing pipeline.

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

Generates synthetic brain MRI volumes using NVIDIA's NV-Generate-CTMR workflow, with configurable modality and random seed.

Generates synthetic CT volumes and masks using NVIDIA's rectified-flow pipeline for medical imaging research.

Provides narrative synthesis, framing, and audience-aware communication patterns to improve decision narratives, written artifacts, and shared understanding.

Curates clinical-specialty term lists, generates IPA-tagged synthetic audio via TTS, and produces NeMo-format manifests for ASR benchmark evaluation.

research-synthesis

Synthesize interviews into themes, contradictions, opportunities, and product implications.

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

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.

娜美（少年漫）认知与表达框架（压缩蒸馏）：航海图天才、财迷喜剧壳、气候战 触发：海贼王 等。虚构

Applied Botany Synthesis Skill

Estimate cell state transitions from unspliced/spliced mRNA dynamics using scVelo, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data.

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.

Diagnosing and fixing bimodal matching score distributions in MaxFuse

Generate knowledge schemas and ontologies from any input format. Extract semantic structures, relationships, and hierarchies. Output as Obsidian markdown with YAML frontmatter, wikilinks, tags, and mermaid diagrams, or export to semantic formats (JSON-LD, RDF, Neo4j Cypher, GraphQL). Supports fractal mode (strict hierarchical constraints) and free mode (flexible generation). Auto-activates for queries containing "schema", "ontology", "knowledge graph", "extract structure", or "generate outline".

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

Botany Synthesis Expert Skill

State-space model with O(n) complexity vs Transformers' O(n²). 5× faster inference, million-token sequences, no KV cache. Selective SSM with hardware-aware design. Mamba-1 (d_state=16) and Mamba-2 (d_state=128, multi-head). Models 130M-2.8B on HuggingFace.

Build and debug Retrieval-Augmented Generation pipelines — chunking, embedding, retrieval, reranking

AI image generation Creative Director powered by Google Gemini Nano Banana models. Use this skill for ANY request involving image creation, editing, visual asset production, or creative direction. Triggers on: generate an image, create a photo, edit this picture, design a logo, make a banner, visual for my anything, and all /banana commands. Handles text-to-image, image editing, multi-turn creative sessions, batch workflows, and brand presets.

Generate images using Google Gemini 3.1 Flash Image Preview via the inference.sh CLI, with support for text-to-image, image editing, multi-image input, and Google Search grounding.

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.