Search: "different"

Performs security-focused differential review of code changes. Adapts analysis depth to codebase size, uses git blame for context, calculates blast radius by counting callers, checks test coverage of modified code, and generates a markdown report. Use when reviewing a PR, commit, or diff for security vulnerabilities, checking whether a change re-introduces a previously fixed bug, asking what else a change could break, or finding which modified code has no test covering it.

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.

Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. Use for variational quantum algorithms, quantum machine learning, simulator validation, and moving validated circuits to provider plugins. For hardware-specific compilation use qiskit or cirq; for open-system dynamics use qutip.

Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. Use for generative modeling, reference mapping, multimodal analysis, or model-based uncertainty; use scanpy for standard preprocessing and exploratory analysis.

Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff. Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification, or building a counts matrix for DESeq2. For single-cell data use scanpy; for statistical fitting alone use pydeseq2.

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".

An open-source long-horizon SuperAgent harness that researches, codes, and creates. With the help of sandboxes, memories, tools, skill, subagents and message gateway, it handles different levels of tasks that could take minutes to hours.

Use when auditing a codebase for semantic duplication - functions that do the same thing but have different names or implementations. Especially useful for LLM-generated codebases where new functions are often created rather than reusing existing ones.

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

PromptyDumpty is a lightweight, universal package manager for AI coding assistant artifacts (prompts, instructions, rules, workflows, etc.). It lets you install and manage prompt packages across different AI coding assistants like GitHub Copilot, Claude, Cursor, Gemini, Windsurf, and more.

Centralized rule set for Cursor AI agents. Rules live in .cursor/rules and guide behavior across different stacks and domains.

Convert editor rules between different AI coding assistants (Cursor, Windsurf, Claude Code, etc.)