Spectre

scimap — Python toolkit for multiplexed imaging spatial single-cell analysis (CODEX, CyCIF, IMC, MIBI, mIHC). Loads MCMICRO quantification CSV outputs into AnnData, performs marker-based hierarchical

3 shared topics • 1 shared operation

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 • 2 shared operations

methylKit -- R/Bioconductor package for DNA methylation analysis from bisulfite sequencing data. Reads Bismark, BSmap, and generic CpG coverage files. Provides differential methylation analysis at bas

1 shared topic • 3 shared operations

QuPath — open-source platform for whole slide image analysis and digital pathology. Provides interactive tools for tissue detection via thresholding, cell detection and positive cell classification (H

2 shared topics • 1 shared operation

Squidpy — spatial single-cell analysis toolkit in the scverse ecosystem for analyzing and visualizing spatial molecular data. Builds spatial neighbor graphs from tissue coordinates (Visium, Xenium, ME

2 shared topics • 1 shared operation