15 projects
zmip
Zoom-in pipeline: per-lineage re-embedding, foreign-lineage scoring and agent refinement of an msp annotation
msp-sc
Multi-sample-pipeline: harmony integration of osp per-sample outputs, cluster QC inspection and cell-type annotation agents, self-contained HTML report
agent-harness-bridge
A small compatibility layer for OpenAI Agents SDK, Claude Agent SDK, and DeepSeek Harness
osp-sc
Agentic single-cell QC and annotation pipeline: per-sample scRNA-seq QC, clustering, DEG, a self-contained HTML report, and an LLM annotation agent
stanhue
Hierarchical auto-coloring for scatter plots with categorical labels
eca-pp
Standardized single-cell preprocessing for the Ensemble Cell Atlas ecosystem
stangene
Gene identifier harmonization for single-cell transcriptomics
stancounts
Recover raw counts from log1p-normalized single-cell expression matrices
standissect-lite
Minor-sibling detection inside existing single-cell clusters — the detection core of standissect, without the heavy stack.
decontx-scanpy
Scanpy-native port of DecontX (Yang et al. 2020) — ambient RNA decontamination for droplet scRNA-seq, validated to machine precision against the upstream Bioconductor kernels.
torchgw
Fast Sampled Gromov-Wasserstein optimal transport solver — pure PyTorch, scalable, differentiable
sjanpy
Subjacent Analysis Toolkits for Single-Cell Omics in Python
scgraph-bench
A tool for evalauting single-cell embeddings using graph-based relations
depair
A scanpy-based single-cell crosstalk analysis package
D2R
A new statistic for efficient detection of repetitive sequences
