SingleCellExperiment

WARP (WDL Analysis Research Pipelines) — Broad Institute's cloud-optimized collection of genomics pipelines written in WDL (Workflow Description Language). Covers whole-genome sequencing (WGS), whole-

2 shared topics • 2 shared operations

Geneformer — transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-specific gene network analysis. Supports fine-tuning for cell type classification, gene

2 shared topics • 2 shared operations

Use when working with SnapHiC — a computational method for identifying chromatin loops from single-cell Hi-C data. SnapHiC processes sparse single-cell contact maps, normalizes for distance decay and

2 shared topics • 2 shared operations

Zarr — chunked, compressed N-dimensional array storage for large numerical datasets in bioinformatics and scientific computing. Supports cloud-native storage (S3, GCS, Azure), parallel read/write, and

2 shared topics • 2 shared operations

BERN2 (Biomedical Entity Recognition and Normalization 2) is a biomedical NLP tool for named entity recognition and normalization in free text and PubMed abstracts. Identifies and normalizes genes, di

1 shared topic • 3 shared operations