Broad WARP Pipelines

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 • 1 shared operation

liger (rliger) -- R package for integrative non-negative matrix factorization (iNMF) of single-cell multi-omic data. Integrates scRNA-seq, scATAC-seq, spatial transcriptomics, and methylation datasets

2 shared topics

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

2 shared topics

STARmap (Spatially-resolved Transcript Amplicon Readout mapping) — in situ spatial transcriptomics method that combines hydrogel-tissue chemistry with sequencing-by-hybridization (SEDAL) for multiplex

2 shared topics

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

2 shared topics