scimap

Spectre is an R toolkit for high-dimensional single-cell cytometry and imaging analysis, including data import (CSV/FCS), metadata integration, arcsinh/logicle transformation, clustering (FlowSOM, Phe

3 shared topics • 1 shared operation

BPCells is a high-performance toolkit for large single-cell RNA-seq and ATAC-seq datasets. Use it when the user mentions BPCells, disk-backed sparse matrices, bitpacked single-cell storage, large 10x

2 shared topics • 2 shared operations

CellPhoneDB — repository of curated receptors, ligands, and their interactions for cell-cell communication analysis from single-cell RNA-seq data. Performs permutation-based statistical analysis (stat

2 shared topics • 2 shared operations

Use this skill for SCTransform normalization of single-cell RNA-seq count matrices. Route here when users ask about variance stabilizing transformation (VST), regularized negative binomial regression

1 shared topic • 3 shared operations

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 • 1 shared operation