Pairpot: a database with real-time lasso-based analysis tailored for paired single-cell and spatial transcriptomics.

Paired single-cell and spatially resolved transcriptomics (SRT) data supplement each other, providing in-depth insights into biological processes and disease mechanisms. Previous SRT databases have limitations in curating sufficient single-cell and SRT pairs (SC-SP pairs) and providing real-time heuristic analysis, which hinder the effort to uncover potential biological insights. Here, we developed Pairpot (http://pairpot.

NeoTCR: an immunoinformatic database of experimentally-supported functional neoantigen-specific TCR sequences.

Neoantigen-based immunotherapy has demonstrated long-lasting antitumor activity. The recognition of neoantigens by T cell receptors (TCRs) is considered a trigger for antitumor responses. Due to the overwhelming number of TCR repertoires in the human genome, pinpointing neoantigen-specific TCRs is a formidable challenge.

Precise detection of cell-type-specific domains in spatial transcriptomics.

Cell-type-specific domains are the anatomical domains in spatially resolved transcriptome (SRT) tissues where particular cell types are enriched coincidentally. It is challenging to use existing computational methods to detect specific domains with low-proportion cell types, which are partly overlapped with or even inside other cell-type-specific domains. Here, we propose De-spot, which synthesizes segmentation and deconvolution as an ensemble to generate cell-type patterns, detect low-proportion cell-type-specific domains, and display these domains intuitively.

SCDD: a novel single-cell RNA-seq imputation method with diffusion and denoising.

Single-cell sequencing technologies are widely used to discover the evolutionary relationships and the differences in cells. Since dropout events may frustrate the analysis, many imputation approaches for single-cell RNA-seq data have appeared in previous attempts. However, previous imputation attempts usually suffer from the over-smooth problem, which may bring limited improvement or negative effect for the downstream analysis of single-cell RNA-seq data.