🧬 gget enables efficient querying of genomic reference databases
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
GEfetch2R - Access Single-cell/Bulk RNA-seq Data from Public Repositories and Benchmark the Subsequent Format Conversion Tools
Zytome is declarative library for handling gene expression data for various data portals or datasets.
Privacy-preserving federated tensor decomposition of single-cell immune data: recovers multicellular programs (donor x cell-type x gene) across institutions by sharing only a program subspace, provably equivalent to pooling and secure-aggregation-compatible.
Data preparation and pretraining pipeline for the scUNVEIL single-cell RNA-seq foundation model.
MCP server for CZ CELLxGENE Discover Census. Single-cell RNA-seq queries, ontology-aware (CL, UBERON, EFO), provenance-tracked. For Claude, Cursor, MCP clients.
FAIR single-cell RNA-seq pipeline mapping nerve–tumour–immune ligand–receptor crosstalk in glioblastoma across 170 donors (CELLxGENE Census, two sequencing-depth arms). Compartment integrity enforced as build gates against a held-out annotation. Snakemake + scvi-tools + scanpy + LIANA + marimo.
Organoid fidelity QC - scRNA-seq organoid vs tissue-reference scoring (marker detection, coverage, aberrant-cluster detection) + Opentrons Flex dosing protocol simulation
Final project for DDLS2024 by Daniil Sarkisyan
Web gateway to browse and explore omics datasets: single-cell data in cellxgene, spatial data in Vitessce, with per-dataset QC reports.
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