Tools

ICRAFT is a web server designed for identifying immune-oncology gene targets. It hosts a comprehensive collection of genome-scale CRISPR screen datasets focused on genes with immune-modulatory functions. Users can leverage ICRAFT to evaluate the effects of specific gene perturbations on immune modulation.
TISMO is a web platform for immunotherapy response evaluation, featuring an extensive repository of data from syngeneic mouse models. It enables users to visualize and analyze immunotherapy efficacy and immune cell infiltration across diverse mouse tumor models.

SPATCH is a spatial transcriptomics database that hosts datasets generated by multiple platforms, including Stereo-seq v3, Visium HD, NanoString 6K, and Xenium 5K. It also includes paired CODEX and scRNA-seq data as references, and provides manually segmented cells as ground truth for training spatial analysis models. Users can visualize and download data directly through the SPATCH interface.
STAGE hosts spatial multi-omics data from 546 female genital tract tumors, including ovarian, endometrial, and cervical cancers. The dataset features Visium HD spatial transcriptomics (n=100), along with whole-exome sequencing, RNA sequencing, whole-genome methylation profiling, microRNA sequencing, and comprehensive clinical annotations.
SOAR is a comprehensive spatial transcriptomics resource that hosts thousands of datasets from six species across 22 tissue types. It provides an interactive interface for visualizing and analyzing spatial transcriptomic profiles across diverse biological contexts.

SPAC-seq is a high-throughput, single-cell resolution spatial CRISPR screening platform compatible with commercially available genome-scale spatial transcriptomic technologies, including Stereo-seq and Visium HD. It enables the functional interrogation of gene perturbations in a spatial context.
Stereo-XCR is a platform designed to retrieve and sequence TCR and BCR repertoires from Stereo-seq cDNA libraries at subcellular resolution. It delivers unbiased, full-length XCR reads alongside spatial transcriptomic data, enabling integrated immune repertoire and spatial expression analysis.

DISSECT is a cell segmentation algorithm that integrates cytological image features with transcriptome-guided fine-tuning to achieve accurate reconstruction of spatial transcriptomes. It is compatible with data generated from platforms such as Stereo-seq, Visium HD, NanoString, and Xenium.
TARDIS is a flexible spatial perturbation analysis toolkit implemented in both Python and R. It applies statistical modeling to identify and prioritize gene perturbations that induce significant spatial repositioning compared to non-targeting controls.