spatial-transcriptomics topic

Tools for computational pathology

Dana-Farber-AIOS

Spatial Single Cell Analysis in Python

scverse

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

dmcable

Bayesian Segmentation of Spatial Transcriptomics Data

kharchenkolab

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

alexisvdb

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

jianhuupenn

Accurate and fast cell marker gene identification with COSG

genecell

Accurate and fast cell marker gene identification with COSG

genecell

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

jfnavarro

Interactive software tool for the assignment of cell types in single-cell studies.

euxhenh