Gardener is an interactive agentic system for single-cell RNA-seq (scRNA-seq) analysis that enables expert-steered, iterative workflows under strict data-residency requirements. Existing large language model (LLM)-based analysis agents commonly encode workflow progress as implicit conversational state and rely on cloud-centric execution, which hinders traceability and auditability and complicates keeping sensitive expression data on-device. Gardener grounds cloud-side reasoning in a local, on-device scientific engine and an Experiment Management Kernel (EMK) that externalizes analysis progress as persistent, immutable snapshots linked by lineage. This explicit state representation supports rollback, branching, and comparison of alternative analysis paths while reusing prior computation. Gardener enforces data isolation by design: cloud-hosted LLMs operate only on snapshot identifiers and sanitized summaries, while raw expression matrices and local artifacts remain on the user’s device. A local graphical user interface (GUI) provides human-in-the-loop steering and inspection of workflow state and outputs. Gardener is released as an open-source desktop application for macOS and Windows under the Apache License 2.0.